These are representative sample records from Science.gov related to your search topic.
For comprehensive and current results, perform a real-time search at Science.gov.
1

USC study finds unique genetic marker may improve detection of recurrent ovarian cancer:  

Cancer.gov

Ovarian cancer is a major health concern for women and the identification of sensitive biomarkers for early detection and/or monitoring of disease recurrence is of high clinical relevance. New work published in the Dec. 7 issue of the online journal PLoS ONE reports promising advances toward the development of blood-based DNA markers for ovarian cancer.

2

Unique among unique. Is it genetically determined?  

PubMed

The cross-country world championship is one of the best models to study characteristics needed to achieve top-level endurance athletic capacity. We report the genotype combination of a recent cross-country champion (12 km race) in polymorphisms of seven genes that are candidates to influence endurance phenotype traits (ACTN3, ACE, PPARGC1A, AMPD1, CKMM, GDF8 (myostatin) and HFE). His data were compared with those of eight other runners (world-class but not world champions). The only athlete with the genotype theoretically more suited to attaining world-class endurance running performance was the case study subject. A favourable genetic endowment, together with exceptional environmental factors (years of altitude living and training in this case), seems to be necessary to attain the highest possible level of running endurance performance. PMID:18662936

Gonzalez-Freire, M; Santiago, C; Verde, Z; Lao, J I; Oiivan, J; Gómez-Gallego, F; Lucia, A

2009-04-01

3

Genetic markers and duodenal ulcer.  

PubMed

Serum pepsinogen, alpha 1-antitrypsin (alpha 1-AT) and blood groups were studied as genetic markers in 32 patients with endoscopically proven duodenal ulcer and 44 control subjects with no family history of ulcer disease. Serum pepsinogen was determined by the modified method of Edward et al, alpha 1-AT by single radial immunodiffusion (RID) and phenotyping was carried out by isoelectric focusing (IEF). Duodenal ulcer patients with hyper- pepsinogenemia (28%) and low serum alpha 1-AT (35%) had a dominant blood group O, lower mean age, an early onset of disease, a higher frequency of gastrointestinal (GI) bleeding and ulcer perforation. These parameters were found considerably different in patients with normal serum pepsinogen and alpha 1-AT. Phenotype analysis of alpha 1-AT revealed that four duodenal ulcer patients had partial deficiency of the protease inhibitor and none of the normal exhibited the deficiency pattern. The etiology of the disease appears to be genetic anomaly in 28% of patients while the rest (72%) had ulcers as a result of neuroendocrinological or environmental factors. PMID:9230579

Shahid, A; Zuberi, S J; Siddiqui, A A; Waqar, M A

1997-05-01

4

Molecular Marker Systems for Oenothera Genetics  

PubMed Central

The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome–genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9·8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed. PMID:18791241

Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G.; Greiner, Stephan

2008-01-01

5

DNA marker technologies and their applications in aquaculture genetics  

Microsoft Academic Search

The development of DNA-based genetic markers has had a revolutionary impact on animal genetics. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. Popular genetic markers in the aquaculture community include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in

Z. J. Liu; J. F. Cordes

2004-01-01

6

Zebrafish Genetic Map with 2000 Microsatellite Markers  

Microsoft Academic Search

The zebrafish is the first vertebrate organism used for large-scale genetic screens seeking genes critical to development. These screens have been quite successful, with more than 1800 recessive mutations discovered that speak to morphogenesis of the vertebrate embryo. The cloning of the mutant genes depends on a dense genetic map. The 2000 markers we present here, using microsatellite (CA) repeats,

Nobuyoshi Shimoda; Ela W. Knapik; John Ziniti; Chäng Sim; Erika Yamada; Stacy Kaplan; Donald Jackson; Frederic de Sauvage; Howard Jacob; Mark C. Fishman

1999-01-01

7

Neutral Genetic Markers and Conservation Genetics: Simulated Germplasm Collections  

Microsoft Academic Search

This study examines the use of neutral genetic markers to guide sampling from a large germplasm collection with the objective of establishing from it a smaller, but genetically representative sample. We simulated evolutionary change and germplasm sampling in a subdivided population of a diploid hermaphrodite annual plant to create an initially large collection. Several strategies of sampling from this collection

Thomas M. Bataillon; Jacques L. David; Daniel J. Schoen

8

Genetic markers on chromosome 7.  

PubMed Central

Chromosome 7 is frequently associated with chromosome aberrations, rearrangements, and deletions. It also contains many important genes, gene families, and disease loci. This brief review attempts to summarise these and other interesting aspects of chromosome 7. With the rapid accumulation of cloned genes and polymorphic DNA fragments, this chromosome has become an excellent substrate for molecular genetic studies. PMID:3290488

Tsui, L C

1988-01-01

9

Genetic Defects as Tumor Markers  

Microsoft Academic Search

Carcinogenesis is long-term multistep accumulation of defects of genes responsible for cell division, DNA repair, and apoptosis. The functions of these genes are known both for norm and for pathologies caused by their damage and resulting in “asocial” cell behavior. Owing to the recent progress in studying the mechanisms of carcinogenesis, some genetic defects may be considered from the applied

A. V. Lichtenstein; G. I. Potapova

2003-01-01

10

Copyright 0 1996 by the Genetics Society of America Neutral Genetic Markers and Conservation Genetics  

E-print Network

Copyright 0 1996 by the Genetics Society of America Neutral Genetic Markers and Conservation- tion in a populationor collection of interest to genetic conservation, making it difficult to proceed: 40!?-417 (Srptemher, 1996) from their results whether a marker-based approach to genetic conservation

Bataillon, Thomas

11

Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: a review.  

PubMed

Sequencing of rice genome has facilitated the understanding of rice evolution and has been utilized extensively for mining of DNA markers to facilitate marker-assisted breeding. Simple sequence repeat (SSR) markers that are tandemly repeated nucleotide sequence motifs flanked by unique sequences are presently the maker of choice in rice improvement due to their abundance, co-dominant inheritance, high levels of allelic diversity, and simple reproducible assay. The current level of genome coverage by SSR markers in rice is sufficient to employ them for genotype identification and marker-assisted selection in breeding for mapping of genes and quantitative trait loci analysis. This review provides comprehensive information on the mapping and applications of SSR markers in investigation of rice cultivars to study their genetic divergence and marker-assisted selection of important agronomic traits. PMID:24915404

Kaur, Shubhneet; Panesar, Parmjit S; Bera, Manab B; Kaur, Varinder

2015-01-01

12

Genetic markers to predict polygenic disease  

Microsoft Academic Search

Many genetic markers that relate to common multifactorial disease in adults have been identified during the past 15 years.\\u000a Their use as adjuncts for the diagnosis, prognosis, prediction of disease or targeting therapy for these disorders has commenced;\\u000a good examples being the Factor V Leiden mutation for venous-thromboembolism, lipoprotein lipase mutations for hypertriglyceridemia\\u000a and the apolipoprotein E4 variant for Alzheimer’s

David J. Galton

1999-01-01

13

Biochemical and genetic markers of erectile dysfunction.  

PubMed

Erectile dysfunction (ED) is a very common pathology, affecting over 150 million men worldwide. The pathogenesis is typically multifactorial, involving a kaleidoscope of organic, endocrine, and psychogenic factors. In general, ED is divided into organic and psychogenic impotence, but most men with organic etiologies have an associated psychogenic component. Given the high frequency of this pathology, the identification of biochemical and genetic correlates and/or markers is of pivotal interest not only for treating preciously these patients and preventing serious psychological consequences but also for the high risk for occult cardiovascular disease (CVD) that often accompanies or follows this pathology. A variety of cardiovascular risk factors have been associated with both the onset and the severity of ED, including markers of endothelial function, thrombosis, and especially dyslipidemia, so that their measurement should now be considered as an important part of the increased global cardiometabolic risk profile in patients with ED. While nitric oxide (NO), asymmetric dimethylarginine (ADMA), and endothelin (ET) hold some promises as biochemical markers of both CVD and ED, there are several technical and clinical drawbacks that make their measurement overall meaningless in the clinical practice. As regards genetic polymorphisms, controversial results have been provided so far. Although some genetic markers were consistently associated with ED, other studies failed to demonstrate significant associations, highlighting a substantial bias in standardization of methodologies and patient enrolment. Nevertheless, further research in this area should be encouraged, since the first promising evidence that gene therapy might be effective to restore the decline in ED has been provided in the animal model. PMID:22870589

Lippi, Giuseppe; Plebani, Mario; Montagnana, Martina; Cervellin, Gianfranco

2012-01-01

14

Optimal use of genetic markers in conservation programmes  

E-print Network

Note Optimal use of genetic markers in conservation programmes Miguel Toro* Luis Silió, Jaime analysed. © Inra/Elsevier, Paris conservation genetics / molecular markers / average coancestry Résumé markers to minimize the homozygosity by descent in a conservation scheme of the Iberian pig. A selection

Boyer, Edmond

15

Genetic Screening: A Unique Game of Survival  

ERIC Educational Resources Information Center

A creative learning game that helps students reinforce basic genetic information and facilitate the identification and understanding of the more subtle issues is presented. The basic framework of the game was conceived by a business major taking non-biology major course 'heredity and society-intertwining legacy.

Kurvink, Karen; Bowser, Jessica

2004-01-01

16

Genetic diversity in European pigs utilizing amplified fragment lenght polymorphism markers. AFLP markers  

Microsoft Academic Search

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism

M. SanCristobal; C. Chevalet; J. Peleman; H. C. M. Heuven; B. W. Brugmans; Schriek van M; R. Joosten; A. P. Rattink; B. Harlizius; M. A. M. Groenen; Y. Amigues; M. Y. Boscher; G. Russell; A. Law; R. Davoli; V. Russo; C. Desautes; L. Alderson; E. Fimland; M. Bagga; J. V. Delgado; J. L. Vega-Pla; A. M. Marinez; M. Ramos; P. Glodek; J. N. Meyer; G. C. Gandini

2006-01-01

17

Modeling the Genetic Architecture of Complex Traits With Molecular Markers  

Microsoft Academic Search

Understanding the genetic control of quantitatively inherited traits is fundamental to agricultural, evolutionary and biomedical genetic research. A detailed picture of the genetic architecture of quantitative traits can be elucidated with a well-saturated genetic map of molecular markers. The parameters that quantify the genetic architecture of a trait include the number of individual quantitative trait loci (QTL), their genomic positions,

Rongling Wu; Wei Hou; Yuehua Cui; Hongying Li; Tian Liu; Song Wu; Chang-Xing Ma; Yanru Zeng

2007-01-01

18

Genetic traceability of black pig meats using microsatellite markers.  

PubMed

Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and -0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10(-14) in population J, 3.17×10(-9) in population B, and 1.03×10(-12) in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers. PMID:25050032

Oh, Jae-Don; Song, Ki-Duk; Seo, Joo-Hee; Kim, Duk-Kyung; Kim, Sung-Hoon; Seo, Kang-Seok; Lim, Hyun-Tae; Lee, Jae-Bong; Park, Hwa-Chun; Ryu, Youn-Chul; Kang, Min-Soo; Cho, Seoae; Kim, Eui-Soo; Choe, Ho-Sung; Kong, Hong-Sik; Lee, Hak-Kyo

2014-07-01

19

Genetic Diversity Among Wheat Cultivars Using Molecular Markers  

Microsoft Academic Search

The objective of this study was to compare amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), and DNA amplification fingerprinting (DAF) marker systems for estimating genetic diversity among 13 Iranian wheat (Triticum aestivum L.) cultivars through average expected heterozygosity (Hav), sum of effective number of alleles (SENA), and marker index (MI). The AFLP markers had the highest values

Babak Abdollahi Mandoulakani; Ali-Akbar Shahnejat-Bushehri; Badredin Ebrahim Sayed Tabatabaei; Sepideh Torabi; Alireza Mohammadi Hajiabad

2010-01-01

20

Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation  

E-print Network

microsatellites or mtDNA. Keywords: amplified fragment length polymorphism (AFLP), conservation genetics, demograContrasting patterns of genetic diversity at three different genetic markers in a marine mammal, WA 99815-6349, USA Abstract Many studies use genetic markers to explore population structure

Dasmahapatra, Kanchon

21

Diversity in Natural Fern Populations: Dominant Markers as Genetic Tools  

Microsoft Academic Search

\\u000a Our aim, in the present chapter, is to provide a synthesis of the use of dominant markers in the Pteridophytes’ genetics.\\u000a We try to provide a ­comprehensive review of the advantages and disadvantages of the selection of dominant markers as genetic\\u000a tools, when compared to other molecular techniques ­available. Dominant markers fulfill most of the ideal characteristics\\u000a of a fingerprinting

E. L. Peredo; A. Revilla; M. Méndez; V. Menéndez; H. Fernández

22

USC researchers link genetic marker to rectal cancer treatment:  

Cancer.gov

A team of University of Southern California researchers has identified a genetic marker that may predict which patients with rectal cancer can be cured by certain chemotherapies when combined with surgery.

23

Apportionment of Genetic Variation in Contemporary Aleut and Eskimo Populations of Alaska Using Anthropometrics and Classical Genetic Markers  

E-print Network

anthropometric measurements and classical genetic markers. Relethford-Blangero method was applied to athropometrics of the study populations. Results were compared to Nei's genetic distance matrix of classical genetic markers. Multivariate analyses were used...

Justice, Anne E.

2007-12-27

24

Characterization of genetic resistance to helminths in goats using microsatellite genetic markers  

E-print Network

CHARACTERIZATION OF GENETIC RESISTANCE TO HELMINTHS IN GOATS USING MICROSATELLITE GENETIC ~RS A Thesis by JOSEPH KAN'GETHE KOGI Submitted to Texas AkM University in partial fulfdiment of the requirements for the degree of MASTER OF SCIENCE... Characterization of Genetic Resistance to Helminths in Goats Using Microsatellite Genetic Markers. (May 1994) Joseph Kan'gethe Kogi, B. V. M. , University of Nairobi Chair of Advisory Committee: Dr. J. R Taylor Twenty-four microsatellite markers, isolated from...

Kogi, Joseph Kan'gethe

2012-06-07

25

Toward Diagnostic and Phenotype Markers for Genetically Transmitted Speech Delay  

ERIC Educational Resources Information Center

Converging evidence supports the hypothesis that the most common subtype of childhood speech sound disorder (SSD) of currently unknown origin is genetically transmitted. We report the first findings toward a set of diagnostic markers to differentiate this proposed etiological subtype (provisionally termed "speech delay-genetic") from other…

Shriberg, Lawrence D.; Lewis, Barbara A.; Tomblin, J. Bruce; McSweeny, Jane L.; Karlsson, Heather B.; Scheer, Alison R.

2005-01-01

26

ORIGINAL ARTICLE Genetic markers for ancestry are correlated with body  

E-print Network

. In practice, the specific ancestry of each genetic locus can be determined and then tested for associationORIGINAL ARTICLE Genetic markers for ancestry are correlated with body composition traits in older European ancestry was assessed in 1,277 African Americans. We found significant correlations between

Reich, David

27

Genetics and biological markers of risk for alcoholism.  

PubMed Central

Substantial scientific evidence has accumulated that both genetic and environmental factors predispose the development of alcoholism in certain individuals. Evidence has accumulated to indicate that alcoholism is a heterogeneous entity arising from multiple etiologies. The demonstrated role of genetics in increasing the risk of alcoholism has promoted the search for biological markers that could objectively identify individuals who are genetically predisposed to alcoholism. Identifying such markers could allow for early diagnosis, focused prevention, and differential and type-specific treatment of alcoholism. Promising markers have been provided by research in electrophysiology, endocrinology, and biochemistry. Recent advances in molecular genetics are offering prospects for direct analysis of the human genome to determine elements that provide predisposition to, and protection from, alcoholism. Recent advances in research and new knowledge gained by the alcoholism treatment community and the lay public are helping to diminish the societal damage caused by alcohol abuse and alcoholism and to change prevailing attitudes about them. PMID:3141966

Tabakoff, B; Hoffman, P L

1988-01-01

28

Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster  

SciTech Connect

For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that have recently revolutionized human, mouse and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila using an STS-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that the genome. The majority of these markers are single nucleotide polymorphisms (SNPs) and sequences for these variants are provided in an accessible format. The average density of the new markers is 1 marker per 225 kb on the autosomes and 1 marker per 1 Mb on the X chromosome. We include in this survey a set of P-element strains that provide additional utility for high-resolution mapping. We demonstrate one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community.

Hoskins, Roger A.; Phan, Alexander C.; Naeemuddin, Mohammed; Mapa, Felipa A.; Ruddy, David A.; Ryan, Jessica J.; Young, Lynn M.; Wells, Trent; Kopczynski, Casey; Ellis, Michael C.

2001-04-16

29

Unique genetic variation at a species' rear edge is under threat from global climate change  

PubMed Central

Global climate change is having a significant effect on the distributions of a wide variety of species, causing both range shifts and population extinctions. To date, however, no consensus has emerged on how these processes will affect the range-wide genetic diversity of impacted species. It has been suggested that species that recolonized from low-latitude refugia might harbour high levels of genetic variation in rear-edge populations, and that loss of these populations could cause a disproportionately large reduction in overall genetic diversity in such taxa. In the present study, we have examined the distribution of genetic diversity across the range of the seaweed Chondrus crispus, a species that has exhibited a northward shift in its southern limit in Europe over the last 40 years. Analysis of 19 populations from both sides of the North Atlantic using mitochondrial single nucleotide polymorphisms (SNPs), sequence data from two single-copy nuclear regions and allelic variation at eight microsatellite loci revealed unique genetic variation for all marker classes in the rear-edge populations in Iberia, but not in the rear-edge populations in North America. Palaeodistribution modelling and statistical testing of alternative phylogeographic scenarios indicate that the unique genetic diversity in Iberian populations is a result not only of persistence in the region during the last glacial maximum, but also because this refugium did not contribute substantially to the recolonization of Europe after the retreat of the ice. Consequently, loss of these rear-edge populations as a result of ongoing climate change will have a major effect on the overall genetic diversity of the species, particularly in Europe, and this could compromise the adaptive potential of the species as a whole in the face of future global warming. PMID:21593035

Provan, Jim; Maggs, Christine A.

2012-01-01

30

Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species  

Microsoft Academic Search

Restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers are being used widely for evaluating genetic relationships of crop germplasm. Differences in the properties of these two markers could result in different estimates of genetic relationships among some accessions. Nuclear RFLP markers detected by genomic DNA and cDNA clones and RAPD markers were compared for evaluating genetic

C. E. Thormann; M. E. Ferreira; L. E. A. Camargo; J. G. Tivang; T. C. Osborn

1994-01-01

31

Genetic Markers and Quantitative Genetic Variation in Medicago Truncatula (Leguminosae): A Comparative Analysis of Population Structure  

PubMed Central

Two populations of the selfing annual Medicago truncatula Gaertn. (Leguminoseae), each subdivided into three subpopulations, were studied for both metric traits (quantitative characters) and genetic markers (random amplified polymorphic DNA and one morphological, single-locus marker). Hierarchical analyses of variance components show that (1) populations are more differentiated for quantitative characters than for marker loci, (2) the contribution of both within and among subpopulations components of variance to overall genetic variance of these characters is reduced as compared to markers, and (3) at the population level, within population structure is slightly but not significantly larger for markers than for quantitative traits. Under the hypothesis that most markers are neutral, such comparisons may be used to make hypotheses about the strength and heterogeneity of natural selection in the face of genetic drift and gene flow. We thus suggest that in these populations, quantitative characters are under strong divergent selection among populations, and that gene flow is restricted among populations and subpopulations. PMID:8844165

Bonnin, I.; Prosperi, J. M.; Olivieri, I.

1996-01-01

32

Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers  

PubMed Central

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (FIT) in native chicken was 0.234±0.025. Over 30.7% of FIT was contributed by within-population deficiency (FIS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds PMID:25178290

Suh, Sangwon; Sharma, Aditi; Lee, Seunghwan; Cho, Chang-Yeon; Kim, Jae-Hwan; Choi, Seong-Bok; Kim, Hyun; Seong, Hwan-Hoo; Yeon, Seong-Hum; Kim, Dong-Hun; Ko, Yeoung-Gyu

2014-01-01

33

Genetic diversity and relationships of korean chicken breeds based on 30 microsatellite markers.  

PubMed

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (F IT) in native chicken was 0.234±0.025. Over 30.7% of F IT was contributed by within-population deficiency (F IS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds. PMID:25178290

Suh, Sangwon; Sharma, Aditi; Lee, Seunghwan; Cho, Chang-Yeon; Kim, Jae-Hwan; Choi, Seong-Bok; Kim, Hyun; Seong, Hwan-Hoo; Yeon, Seong-Hum; Kim, Dong-Hun; Ko, Yeoung-Gyu

2014-10-01

34

DNA marker applications to molecular genetics and genomics in tomato  

PubMed Central

Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178

Shirasawa, Kenta; Hirakawa, Hideki

2013-01-01

35

Genetic markers and population history: Finland revisited  

Microsoft Academic Search

The Finnish population in Northern Europe has been a target of extensive genetic studies during the last decades. The population is considered as a homogeneous isolate, well suited for gene mapping studies because of its reduced diversity and homogeneity. However, several studies have shown substantial differences between the eastern and western parts of the country, especially in the male-mediated Y

Jukka U Palo; Ismo Ulmanen; Matti Lukka; Pekka Ellonen; Antti Sajantila

2009-01-01

36

A polymorphic DNA marker genetically linked to Huntington's disease  

Microsoft Academic Search

Family studies show that the Huntington's disease gene is linked to a polymorphic DNA marker that maps to human chromosome 4. The chromosomal localization of the Huntington's disease gene is the first step in using recombinant DNA technology to identify the primary genetic defect in this disorder.

James F. Gusella; Nancy S. Wexler; P. Michael Conneally; Susan L. Naylor; Mary Anne Anderson; Rudolph E. Tanzi; Paul C. Watkins; Kathleen Ottina; Margaret R. Wallace; Alan Y. Sakaguchi; Anne B. Young; Ira Shoulson; Ernesto Bonilla; Joseph B. Martin

1983-01-01

37

Original article Genetic markers for Prunus avium L.  

E-print Network

Original article Genetic markers for Prunus avium L. 2. Clonal identifications and discrimination from P cerasus and P cerasus x P avium F Santi, M Lemoine INRA, Station d'Amélioration des arbres cherry in wild cherries. Isozyme / Prunus / wild cherry / sour cherry / duke cherry / identification

Paris-Sud XI, Université de

38

GENETIC DIVERSITY OF CARICA PAPAYA AS REVEALED BY AFLP MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genetic relationships among Carica papaya cultivars, breeding lines, unimproved germplasm, and related species were established using amplified fragment length polymorphism (AFLP) markers. Seventy-one papaya accessions and related species were analyzed with nine EcoRI-MseI primer combinations. A t...

39

Genetic diversity analysis in Cymbopogon species using DNA markers  

Microsoft Academic Search

Genetic diversity of 25 accessions of Cymbopogon aromatic grasses including eight species, two hybrids and one mutant strain were analyzed using DNA markers generated by employing 20 primer pairs derived from cDNAs containing simple sequence repeat (SSR) of rice genome. A total of 151 bands were produced ranging from 3 to 12 per primer pair. The polymorphic information content values

J. Kumar; V. Verma; A. Goyal; A. K. Shahi; R. Sparoo; R. S. Sangwan; G. N. Qazi

40

Genetic variation (protein markers and microsatellites) in endangered Catalonian donkeys  

Microsoft Academic Search

Genetic variation of the endangered Catalonian donkey breed (Equus asinus) has been analysed at 19 loci including seven protein loci and 12 microsatellite loci isolated from the domestic horse, in 98 individuals of both sexes. Only four protein markers and three microsatellites were polymorphic. Allele frequencies of the analysed loci showed close agreement with Hardy–Weinberg proportions, with the exception of

J. Jordana; P. Folch; A. Sanchez

1999-01-01

41

Genetic markers cannot determine Jewish descent  

PubMed Central

Humans differentiate, classify, and discriminate: social interaction is a basic property of human Darwinian evolution. Presumably inherent differential physical as well as behavioral properties have always been criteria for identifying friend or foe. Yet, biological determinism is a relatively modern term, and scientific racism is, oddly enough, largely a consequence or a product of the Age of Enlightenment and the establishment of the notion of human equality. In recent decades ever-increasing efforts and ingenuity were invested in identifying Biblical Israelite genotypic common denominators by analysing an assortment of phenotypes, like facial patterns, blood types, diseases, DNA-sequences, and more. It becomes overwhelmingly clear that although Jews maintained detectable vertical genetic continuity along generations of socio-religious-cultural relationship, also intensive horizontal genetic relations were maintained both between Jewish communities and with the gentile surrounding. Thus, in spite of considerable consanguinity, there is no Jewish genotype to identify. PMID:25653666

Falk, Raphael

2015-01-01

42

Genetic Marker Identified for Aggressive Bladder Cancer  

Cancer.gov

Researchers led by Ludmila Prokunina-Olsson, Ph.D., in DCEG's Laboratory of Translational Genomics, have identified the first genetic variant associated with risk of aggressive bladder cancer. The variant, rs7257330, is in the promoter region of the CCNE1 gene, which encodes for cyclin E protein, a cell cycle regulator. This result comes from a fine-mapping analysis of data from two bladder cancer genome-wide association studies and functional studies.

43

Prostate cancer risk-associated genetic markers and their potential clinical utility  

PubMed Central

Prostate cancer (PCa) is one of the most common cancers among men in Western developed countries and its incidence has increased considerably in many other parts of the world, including China. The etiology of PCa is largely unknown but is thought to be multifactorial, where inherited genetics plays an important role. In this article, we first briefly review results from studies of familial aggregation and genetic susceptibility to PCa. We then recap key findings of rare and high-penetrance PCa susceptibility genes from linkage studies in PCa families. We devote a significant portion of this article to summarizing discoveries of common and low-penetrance PCa risk-associated single-nucleotide polymorphisms (SNPs) from genetic association studies in PCa cases and controls, especially those from genome-wide association studies (GWASs). A strong focus of this article is to review the literature on the potential clinical utility of these implicated genetic markers. Most of these published studies described PCa risk estimation using a genetic score derived from multiple risk-associated SNPs and its utility in determining the need for prostate biopsy. Finally, we comment on the newly proposed concept of genetic score; the notion is to treat it as a marker for genetic predisposition, similar to family history, rather than a diagnostic marker to discriminate PCa patients from non-cancer patients. Available evidence to date suggests that genetic score is an objective and better measurement of inherited risk of PCa than family history. Another unique feature of this article is the inclusion of genetic association studies of PCa in Chinese and Japanese populations. PMID:23564047

Xu, Jianfeng; Sun, Jielin; Zheng, S Lilly

2013-01-01

44

Copyright 1999 by the Genetics Society of America Estimation of Pairwise Relatedness With Molecular Markers  

E-print Network

Applications of quantitative genetics and conservation genetics often require measures of pairwise marker-field of conservation genetics. For example, in captive based estimators for wCopyright © 1999 by the Genetics Society of America Estimation of Pairwise Relatedness

Lynch, Michael

45

[Molecular-genetic markers in lung cancer diagnostics].  

PubMed

The major approaches to different lung cancer marker development are outlined in the review, including genetic, epigenetic, protein, transcryptomic, proteomic, metabolic, and miRNA markers. As far as epigenetic changes are among the earliest events in malignant transformation, methylated markers are thoroughly discussed. Special attention is given to minimally invasive tumor markers, which could be detected in easily accessible biological fluids, because they can be useful for screening and early diagnostics of cancer (before its clinical manifestation) as well as for verification of standard methods of diagnostics. Extracellular nucleic acids, circulating in blood (cirNA), are highlighted as the potential source of material for the early lung cancer diagnostics, prediction of antitumor treatment efficiency, post-treatment monitoring and disease prognosis. PMID:21634110

Ponomareva, A A; Rykova, E Iu; Cherdyntseva, N V; Cho?nzonov, E L; Laktionov, P P; Vlasov, V V

2011-01-01

46

INSL5 may be a unique marker of colorectal endocrine cells and neuroendocrine tumors  

SciTech Connect

Highlights: ? INSL5 is expressed in enteroendocrine cells along the colorectum. ? INSL5 is expressed increasingly from proximal colon to rectum. ? INSL5 co-localizes rarely with chromogranin A. ? All rectal neuroendocrine tumors examined expressed INSL5. -- Abstract: Insulin-like peptide 5 (INSL5) is a member of the insulin superfamily, and is a potent agonist for RXFP4. We have shown that INSL5 is expressed in enteroendocrine cells (EECs) along the colorectum with a gradient increase toward the rectum. RXFP4 is ubiquitously expressed along the digestive tract. INSL5-positive EECs have little immunoreactivity to chromogranin A (CgA) and might be a unique marker of colorectal EECs. CgA-positive EECs were distributed normally along the colorectum in INSL5 null mice, suggesting that INSL5 is not required for the development of CgA-positive EECs. Exogenous INSL5 did not affect the proliferation of human colon cancer cell lines, and chemically-induced colitis in INSL5 null mice did not show any significant changes in inflammation or mucosal healing compared to wild-type mice. In contrast, all of the rectal neuroendocrine tumors examined co-expressed INSL5 and RXFP4. INSL5 may be a unique marker of colorectal EECs, and INSL5–RXFP4 signaling might play a role in an autocrine/paracrine fashion in the colorectal epithelium and rectal neuroendocrine tumors.

Mashima, Hirosato, E-mail: hmashima1-tky@umin.ac.jp [Department of Gastroenterology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543 (Japan)] [Department of Gastroenterology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543 (Japan); Ohno, Hideki [Division of Advanced Medical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan)] [Division of Advanced Medical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Yamada, Yumi; Sakai, Toshitaka; Ohnishi, Hirohide [Department of Gastroenterology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543 (Japan)] [Department of Gastroenterology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543 (Japan)

2013-03-22

47

Genetic analysis of cystic fibrosis using linked DNA markers.  

PubMed Central

Genetic linkage has been analyzed between cystic fibrosis (CF) and a number of markers on the long arm of chromosome 7, including D7S15, COL1A2, PON, MET, D7S8, and TCRB, using a cohort of 47 Canadian and 13 Danish CF families. The analysis confirms the previous observations that both MET and D7S8 are closely linked to CF. Based on the result from one family, MET appears to be more proximal to the centromere than CF. Our analysis also suggests that genetic heterogeneity may account for the high recombination fraction between CF and D7S8 observed in another family. In addition, a strong linkage disequilibrium has been observed between CF and the two closely flanking markers. PMID:3467587

Tsui, L C; Buetow, K; Buchwald, M

1986-01-01

48

Major histocompatibility locus genetic markers of beryllium sensitization and disease  

Microsoft Academic Search

Major histocompatibility locus genetic markers of beryllium sensitization and disease. C. Saltini, L. Richeldi, M. Losi, M. Amicosante, C. Voorter, E. van den Berg-Loonen, R.A. Dweik, H.P. Wiedemann, D.C. Deubner, C. Tinelli. #ERS Journals Ltd 2001. ABSTRACT: Hypersensitivity to beryllium (Be) is found in 1-16% of exposed workers undergoing immunological screening for beryllium disease using the beryllium lym- phocyte proliferation

C. Saltini; L. Richeldi; M. Losi; M. Amicosante; C. Voorter; E. Van Den Berg-Loonen; R. A. Dweik; H. P. Wiedemann; D. C. Deubner; C. Tinelli

2001-01-01

49

Neural Markers of Genetic Vulnerability to Drug Addiction  

Microsoft Academic Search

\\u000a This chapter will summarize genetics findings derived from various strategies and highlight important neural markers (or correlates)\\u000a in some specific and extensively studied genes. Most studies highlighted here focus on alcohol and nicotine dependence (AD\\u000a and ND, respectively). AD and ND are among the most prevalent addictive disorders worldwide, are among the best studied, and\\u000a are also associated globally with

Daniel J. Müller; Olga Likhodi; Andreas Heinz

50

Assessment of genetic diversity in Azadirachta indica using AFLP markers  

Microsoft Academic Search

Genetic diversity was estimated in 37 neem accessions from different eco-geographic regions of India and four exotic lines\\u000a from Thailand using AFLP markers. Seven AFLP selective primer combinations generated a total of 422 amplification products.\\u000a The average number of scorable fragments was 60 per experiment, and a high degree (69.8%) of polymorphism was obtained per\\u000a assay with values ranging from

A. Singh; M. S. Negi; J. Rajagopal; S. Bhatia; U. K. Tomar; P. S. Srivastava; M. Lakshmikumaran

1999-01-01

51

Genetic Kinship Investigation from Blood Groups to DNA Markers.  

PubMed

The forensic application of hereditary characteristics became possible after the discovery of human blood groups by Karl Landsteiner in 1901. The foundation for their use in kinship investigation was laid by Emil von Dungern and Ludwig Hirschfeld in 1910 by clarification of the inheritance of the ABO groups. Up to the middle of the 20th century further red cell membrane systems were discovered. From the 1920s Fritz Schiff and Georg Strassmann fought for the introduction of blood groups into forensic kinship investigation. A new era of hemogenetics was opened from 1955 as genetic polymorphisms were described in serum proteins. Starting in 1958 there followed the complex HLA system of white blood cells, which from 1963 was joined by polymophisms in erythrocyte enzymes. Therefore, from the 1980s, it was possible to clarify the majority of kinship cases with a combination of conventional markers. From 1990 to 2000 the conventional markers were gradually replaced by the more effective DNA markers. Simultaneously typing shifted from the phenotype level to the genotype level. The genomic structure of conventional genetic markers could also now be explained. As a reflection of scientific progress the legal situation also changed, particularly in the form of the official guidelines for kinship investigation. PMID:22851931

Geserick, Gunther; Wirth, Ingo

2012-06-01

52

Genetic Kinship Investigation from Blood Groups to DNA Markers  

PubMed Central

The forensic application of hereditary characteristics became possible after the discovery of human blood groups by Karl Landsteiner in 1901. The foundation for their use in kinship investigation was laid by Emil von Dungern and Ludwig Hirschfeld in 1910 by clarification of the inheritance of the ABO groups. Up to the middle of the 20th century further red cell membrane systems were discovered. From the 1920s Fritz Schiff and Georg Strassmann fought for the introduction of blood groups into forensic kinship investigation. A new era of hemogenetics was opened from 1955 as genetic polymorphisms were described in serum proteins. Starting in 1958 there followed the complex HLA system of white blood cells, which from 1963 was joined by polymophisms in erythrocyte enzymes. Therefore, from the 1980s, it was possible to clarify the majority of kinship cases with a combination of conventional markers. From 1990 to 2000 the conventional markers were gradually replaced by the more effective DNA markers. Simultaneously typing shifted from the phenotype level to the genotype level. The genomic structure of conventional genetic markers could also now be explained. As a reflection of scientific progress the legal situation also changed, particularly in the form of the official guidelines for kinship investigation. PMID:22851931

Geserick, Gunther; Wirth, Ingo

2012-01-01

53

On coding genotypes for genetic markers with multiple alleles in genetic association study of quantitative traits  

PubMed Central

Background In genetic association study of quantitative traits using F? models, how to code the marker genotypes and interpret the model parameters appropriately is important for constructing hypothesis tests and making statistical inferences. Currently, the coding of marker genotypes in building F? models has mainly focused on the biallelic case. A thorough work on the coding of marker genotypes and interpretation of model parameters for F? models is needed especially for genetic markers with multiple alleles. Results In this study, we will formulate F? genetic models under various regression model frameworks and introduce three genotype coding schemes for genetic markers with multiple alleles. Starting from an allele-based modeling strategy, we first describe a regression framework to model the expected genotypic values at given markers. Then, as extension from the biallelic case, we introduce three coding schemes for constructing fully parameterized one-locus F? models and discuss the relationships between the model parameters and the expected genotypic values. Next, under a simplified modeling framework for the expected genotypic values, we consider several reduced one-locus F? models from the three coding schemes on the estimability and interpretation of their model parameters. Finally, we explore some extensions of the one-locus F? models to two loci. Several fully parameterized as well as reduced two-locus F? models are addressed. Conclusions The genotype coding schemes provide different ways to construct F? models for association testing of multi-allele genetic markers with quantitative traits. Which coding scheme should be applied depends on how convenient it can provide the statistical inferences on the parameters of our research interests. Based on these F? models, the standard regression model fitting tools can be used to estimate and test for various genetic effects through statistical contrasts with the adjustment for environmental factors. PMID:21936918

2011-01-01

54

Genetic relationships between Lolium (Poaceae) species revealed by RAPD markers.  

PubMed

The genus Lolium is one of the most important groupings of temperate forage grasses, including about eight recognized species that are native to some temperate and subtropical regions of the northern hemisphere. We examined genetic relationships among 18 accessions representing all Lolium species using RAPD markers. Among 50 random primers that we screened, 13 gave reproducible amplification banding patterns. Each of these 13 primers generated 19-43 scorable fragments. A total of 367 RAPD fragments were detected, of which 95.9% were polymorphic across all the Lolium accessions. Dice's coefficient of dissimilarity ranged from 0.016 to 0.622, which is indicative of substantial genetic variations in these Lolium accessions. A neighbor-joining cluster analysis, with bootstrap permutation, produced an unrooted dendrogram, which grouped 18 accessions into two main clades, supporting high bootstrap values (98 and 96%). The first clade included the self-pollinated species, L. persicum, L. temulentum, L. remotum, and L. subulatum. The cross-pollinated species, i.e., L. multiflorum, L. perenne, L. rigidum, and L. canariense, composed the second clade, in which L. canariense formed a distinct subclade, indicating its higher genetic separation from other allogamous species. The value of r = 0.97 in the Mantel test for cophenetic correlation applied to the cluster analysis indicated the high degree of fit of the accessions to a group. A principal coordinate analysis, whose first three coordinates explained 72.6% of the variation, showed similar groupings as in the cluster analysis. The genetic relationships estimated by the polymorphism of RAPD markers are basically in agreement with those previously inferred with other genetic markers. PMID:23546973

Ma, X; Gu, X-Y; Chen, T-T; Chen, S-Y; Huang, L-K; Zhang, X-Q

2013-01-01

55

Genetic diversity in tetraploid switchgrass revealed by AFLP marker polymorphisms.  

PubMed

Switchgrass (Panicum virgatum) is a perennial warm-season grass native to North America that has been identified as a dedicated cellulosic biofuel crop. We quantified genetic diversity in tetraploid switchgrass germplasm collected at Oklahoma State University and characterized genetic relatedness among the collections from distinct regions. Fifty-six tetraploid accessions, including seven upland and 49 lowland genotypes from throughout the US, were examined. The amplified fragment length polymorphism (AFLP) procedure was utilized to generate DNA profiling patterns that were scored visually. Sixteen selective AFLP primer combinations were used to amplify 452 polymorphic bands. The accessions' genetic similarity coefficients, UPGMA (unweighted pair-group method with arithmetic averaging) cluster analysis and principle coordinate analysis, were performed. The upland and lowland accessions clustered according to ecotypes, with one exception (TN104). Genetic similarity coefficients among the accessions ranged from 0.73 to 0.95. Analysis of molecular variance (AMOVA) was performed, showing significant differences between the upland and lowland genotypes. The trnL marker confirmed that TN104 was a lowland genotype, but the trnL marker identification of upland and lowland genotypes was not consistent with the AFLP analysis in two germplasms (Miami and AR4). PMID:22180031

Todd, J; Wu, Y Q; Wang, Z; Samuels, T

2011-01-01

56

IDENTIFICATION OF CACAO TIR-NBS-LRR RESISTANCE GENE ANALOGS AND THEIR USE AS GENETIC MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Identifying genetic markers linked to disease resistance in plants is an important goal in marker assisted selection. Using a candidate gene approach, we have developed genetic markers for non-TIR-NBS-LRR resistance gene analogs and WRKY transcription factor genes, both families involved in disease...

57

Genetic diversity analysis of common beans based on molecular markers  

PubMed Central

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

Gill-Langarica, Homar R.; Muruaga-Martínez, José S.; Vargas-Vázquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

2011-01-01

58

Applicability of bovine microsatellite markers for population genetic studies on African buffalo (Syncerus caffer)  

Microsoft Academic Search

The applicability of bovine autosomal micro- satellite markers for population genetic studies on African buffalo was investigated. A total of 168 microsatellite markers were tested for PCR amplification on a test panel of seven African buffalo. Amplification was observed for 139 markers (83%), and 101 markers were studied further with 91 (90%) being polymorphic. The mean number of alleles per

Hooft van W. F; O. Hanotte; P. W. Wenink; A. F. Groen; Y. Sugimoto; H. H. T. Prins; A. Teale

1999-01-01

59

Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers.  

PubMed

Basque people have received considerable attention from anthropologists, geneticists, and linguists during the last century due to the singularity of their language and to other cultural and biological characteristics. Despite the multidisciplinary efforts performed to address the questions of the origin, uniqueness, and heterogeneity of Basques, the genetic studies performed up to now have suffered from a weak study design where populations are not analyzed in an adequate geographic and population context. To address the former questions and to overcome these design limitations, we have analyzed the uniparentally inherited markers (Y chromosome and mitochondrial DNA) of ~900 individuals from 18 populations, including those where Basque is currently spoken and populations from adjacent regions where Basque might have been spoken in historical times. Our results indicate that Basque-speaking populations fall within the genetic Western European gene pool, that they are similar to geographically surrounding non-Basque populations, and also that their genetic uniqueness is based on a lower amount of external influences compared with other Iberians and French populations. Our data suggest that the genetic heterogeneity and structure observed in the Basque region result from pre-Roman tribal structure related to geography and might be linked to the increased complexity of emerging societies during the Bronze Age. The rough overlap of the pre-Roman tribe location and the current dialect limits support the notion that the environmental diversity in the region has played a recurrent role in cultural differentiation and ethnogenesis at different time periods. PMID:22411853

Martínez-Cruz, Begoña; Harmant, Christine; Platt, Daniel E; Haak, Wolfgang; Manry, Jeremy; Ramos-Luis, Eva; Soria-Hernanz, David F; Bauduer, Frédéric; Salaberria, Jasone; Oyharçabal, Bernard; Quintana-Murci, Lluis; Comas, David

2012-09-01

60

[Immunochemical and molecular-genetic markers in gastric cancer diagnostics].  

PubMed

Studies of molecular mechanisms of neoplastic transfromation are being under the thorough investigation, reveal the new genes involved into the tumor development. These genes and their products are potential tumor markers and levels of their expression can be detected using modem assays characterized by high specificity and sensitivity. The review highlights the current status of the molecular diagnostics of gastric cancer, including protein and nucleic acids biomarkers. The genetic and epigenetic changes, which are detected in the malignant and nonmalignant tumor tissue DNA and in the blood plasma DNA from tumor bearing patients, are summarized. PMID:19351030

Elistratova, E P; Laktionov, P P; Shelestiuk, P I; Tuzikov, S A; Vlasov, V V; Rykova, E Iu

2009-01-01

61

Texas Adapted Genetic Strategies for Beef Cattle--11: Marker Assisted Selection for Beef Improvement  

E-print Network

This publication is Number 11 in the series "Texas Adapted Genetic Strategies for Beef Cattle. Bits of DNA called markers can be useful in determining possible specific performance of a particular trait; these markers are typically located near...

Paschal, Joseph C.

2005-07-15

62

The Unique hmuY Gene Sequence as a Specific Marker of Porphyromonas gingivalis  

PubMed Central

Porphyromonas gingivalis, a major etiological agent of chronic periodontitis, acquires heme from host hemoproteins using the HmuY hemophore. The aim of this study was to develop a specific P. gingivalis marker based on a hmuY gene sequence. Subgingival samples were collected from 66 patients with chronic periodontitis and 40 healthy subjects and the entire hmuY gene was analyzed in positive samples. Phylogenetic analyses demonstrated that both the amino acid sequence of the HmuY protein and the nucleotide sequence of the hmuY gene are unique among P. gingivalis strains/isolates and show low identity to sequences found in other species (below 50 and 56%, respectively). In agreement with these findings, a set of hmuY gene-based primers and standard/real-time PCR with SYBR Green chemistry allowed us to specifically detect P. gingivalis in patients with chronic periodontitis (77.3%) and healthy subjects (20%), the latter possessing lower number of P. gingivalis cells and total bacterial cells. Isolates from healthy subjects possess the hmuY gene-based nucleotide sequence pattern occurring in W83/W50/A7436 (n?=?4), 381/ATCC 33277 (n?=?3) or TDC60 (n?=?1) strains, whereas those from patients typically have TDC60 (n?=?21), W83/W50/A7436 (n?=?17) and 381/ATCC 33277 (n?=?13) strains. We observed a significant correlation between periodontal index of risk of infectiousness (PIRI) and the presence/absence of P. gingivalis (regardless of the hmuY gene-based sequence pattern of the isolate identified [r?=?0.43; P?=?0.0002] and considering particular isolate pattern [r?=?0.38; P?=?0.0012]). In conclusion, we demonstrated that the hmuY gene sequence or its fragments may be used as one of the molecular markers of P. gingivalis. PMID:23844074

Mackiewicz, Pawe?; Radwan-Oczko, Ma?gorzata; Kantorowicz, Ma?gorzata; Chomyszyn-Gajewska, Maria; Fr?szczak, Magdalena; Bielecki, Marcin; Olczak, Mariusz; Olczak, Teresa

2013-01-01

63

Senescence marker protein-30 is a unique enzyme that hydrolyzes diisopropyl phosphorofluoridate in the liver.  

PubMed

Senescence marker protein-30 (SMP30) was originally identified as a novel protein in the rat liver, the expression of which decreases androgen-independently with aging. We have now characterized a unique property of SMP30, the hydrolysis of diisopropyl phosphorofluoridate (DFP), which is similar to the chemical warfare nerve agents sarine, soman and tabun. Hydrolysis of DFP was stimulated equally well by 1 mM MgCl2, MnCl2 or CoCl2, to a lesser extent by 1 mM CdCl2 but not at all by 1 mM CaCl2. No 45Ca2+-binding activity was detected for purified SMP30, suggesting that SMP30 is not a calcium-binding protein, as others previously stated. Despite the sequence similarity between SMP30 and a serum paraoxonase (PON), the inability of SMP30 to hydrolyze PON-specific substrates such as paraoxon, dihydrocoumarin, gamma-nonalactone, and delta-dodecanolactone indicate that SMP30 is distinct from the PON family. We previously established SMP30 knockout mice and have now tested DFPase activity in their livers. The livers from wild-type mice contained readily detectable DFPase activity, whereas no such enzyme activity was found in livers from SMP30 knockout mice. Moreover, the hepatocytes of SMP30 knockout mice were far more susceptible to DFP-induced cytotoxicity than those from the wild-type. These results indicate that SMP30 is a unique DFP hydrolyzing enzyme in the liver and has an important detoxification effect on DFP. Consequently, a reduction of SMP30 expression might account for the age-associated deterioration of cellular functions and enhanced susceptibility to harmful stimuli in aged tissue. PMID:15251439

Kondo, Yoshitaka; Ishigami, Akihito; Kubo, Sachiho; Handa, Setsuko; Gomi, Keiko; Hirokawa, Kozo; Kajiyama, Naoki; Chiba, Tsuyoshi; Shimokado, Kentaro; Maruyama, Naoki

2004-07-16

64

Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis.  

PubMed

Japanese population of the Japanese crested ibis Nipponia nippon was founded by five individuals gifted from the People's Republic of China. In order to exactly evaluate genetic structure, we first performed development of novel genetic makers using 89 microsatellite primer pairs of related species for cross-amplification. Of these, only three primer pairs were useful for the genetic markers. Additionally, we sequenced allelic PCR products of these three markers together with 10 markers previously identified. Most markers showed typical microsatellite repeat units, but two markers were not simple microsatellites. Moreover, over half of the markers did not have the same repeat units as those of the original species. These results suggested that development of novel genetic markers in this population by cross-amplification is not efficient, partly because of low genetic diversity. Furthermore, the cluster analysis by STRUCTURE program using 17 markers showed that the five founders were divided into two clusters. However, the genetic relationships among the founders indicated by the clustering seemed to be questionable, because the analysis relied largely on a small number of triallelic markers, in spite of the addition of the three useful markers. Therefore, more efficient methods for identifying large numbers of single nucleotide polymorphisms are desirable. PMID:24330458

Tsubono, Kanako; Taniguchi, Yukio; Matsuda, Hirokazu; Yamada, Takahisa; Sugiyama, Toshie; Homma, Kosuke; Kaneko, Yoshinori; Yamagishi, Satoshi; Iwaisaki, Hiroaki

2014-04-01

65

Genetic divergence among sweet corn lines estimated by microsatellite markers.  

PubMed

The purpose of this study was to analyze the genetic diversity of 15 sugary-1 sweet corn lines by microsatellite markers. One hundred pairs of simple sequence repeat primers that were mapped for field corn were tested. Of these primers, 15% were polymorphic, and all were selected for the evaluation. These primers identified a total of 39 alleles among the 15 loci that were evaluated. The number of alleles per locus in the genotypes ranged from 2 to 4, with an average of 2.60 alleles per locus; the highest number of alleles was observed at the loci Bnlg1083, Umc1241, and Umc1590. The occurrence of null alleles at locus Umc1363 was evident only in line DN44. The proportion of polymorphic loci was the highest in lines DN17.1 and DN6 (73.33%), whereas lines DN47, DN23, and DN28 were more monomorphic than other lines. The loci Bnlg1083 and Umc1506 were polymorphic in 8 and 7 lines, respectively, indicating that these loci might be effective and promising for the identification of polymorphism in other sweet corn lines. The genetic diversity calculated by Rogers' genetic distances indicated the lowest genetic similarity between lines DN9 and DN28 (0.7603) and the highest similarity between lines DN19 and DN6 (0.3724). The dendrogram obtained by the unweighted pair-group method based on arithmetic averages indicated the formation of 4 major groups, showing the crossing of the genotypes DN19 and DN6 with DN8 as a possible alternative for the expression of heterozygosis. PMID:25511025

Lopes, A D; Scapim, C A; Mangolin, C A; Machado, M F P S

2014-01-01

66

Evaluating the Genetic Diversity of Triticale with Wheat and Rye SSR Markers  

Microsoft Academic Search

Triticale (3Triticosecale Wittmack) is becoming increasingly im- portant in agriculture and understanding its genetic diversity is es- sential for its continued improvement. Simple sequence repeat (SSR) markers are highly polymorphic and widely used for genetic diversity studies. Previous genetic diversity studies using SSRs have focused on the European winter triticale gene pool. Our objective was to investi- gate the genetic

C. Kuleung; P. S. Baenziger; S. D. Kachman; I. Dweikat

2006-01-01

67

Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics  

Microsoft Academic Search

The aim of the present work was to develop a microsatellite marker-based map of the Vitis vinifera genome ( n=19), useful for genetic studies in this perennial heterozygous species, as SSR markers are highly transferable co-dominant markers. A total of 346 primer pairs were tested on the two parents (Syrah and Grenache) of a full sib population of 96 individuals

A.-F. Adam-Blondon; C. Roux; D. Claux; G. Butterlin; D. Merdinoglu; P. This

2004-01-01

68

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis  

E-print Network

in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove). Key wordsInferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full framework for estimating species trees and species demograph- ics from genetic markers. However, practical

Rosenberg, Noah

69

Identification of genetic markers to distinguish the virulent and avirulent subspecies of Pantoea stewartii by comparative proteomics and genetic analysis.  

PubMed

Pantoea stewartii subsp. stewartii (Pnss), the causal agent of Stewart's bacterial wilt and leaf blight of maize and sweet corn, is one of the quarantine pathogens in many countries and regions. In contrast, P. stewartii subsp. indologenes (Pnsi), the closely related subspecies of Pnss, is avirulent on these plants. In this study, the protein expression profiles of these two subspecies were compared using two-dimensional gel electrophoresis analysis. Twenty-one unique protein spots consistently detected in Pnss but not in Pnsi were analyzed by mass spectrometry. Some of these Pnss-specific proteins are known to be essential for virulence and survival in host, such as FoxR and HrcJ, which are the key components of iron uptake and Type III secretion systems, respectively. For further genetic analysis, six Pnss-specific proteins were characterized by peptide sequencing. Southern and Northern blot analyses revealed that the differences in protein expression profiles of the two subspecies were either due to the discrepancy at genome level or because of the variations in transcriptional expression. The results provide novel genetic markers to distinguish the two closely related subspecies and may also serve as useful clues for investigation of the genetic basis accounting for their sharp difference in virulence. PMID:17086414

Wu, Qiong; Jiang, Zide; Liao, Jinliang; Chen, Zhinan; Li, Huaping; Mei, Mantong; Zhang, Lian-Hui

2007-02-01

70

Genetic diversity in European chestnut populations by means of genomic and genic microsatellite markers  

Microsoft Academic Search

Microsatellite or simple sequence repeats (SSRs) are one of the most used markers in population genetic studies. SSR markers\\u000a developed from expressed sequence tags (EST) have proved useful to examine functional diversity in relation to adaptive variation.\\u000a The information provided by both genomic and genic microsatellite markers could offer more accurate indication on the distribution\\u000a of the genetic diversity among

M. Angela Martin; Claudia Mattioni; Marcello Cherubini; Daniela Taurchini; Fiorella Villani

2010-01-01

71

A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers.  

PubMed

Using a population of 105 interspecific F(2) hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. 'Fairway' as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future. PMID:22462407

Yu, Xiaoxia; Li, Xiaolei; Ma, Yanhong; Yu, Zhuo; Li, Zaozhe

2012-03-30

72

The genetic signature of perineuronal oligodendrocytes reveals their unique phenotype  

PubMed Central

Oligodendrocytes – best known for assembling central nervous system myelin – can be categorized as precursors, myelin-forming cells and non-myelinating perineuronal cells. Perineuronal oligodendrocytes have been well characterized morphologically and ultrastructurally, but knowledge about their function remains scanty. It has been proposed that perineuronal oligodendrocytes support neurons and, following injury, transform into myelin-synthesizing cells. Recent findings implicating perineuronal oligodendrocytes in cytoarchitectural abnormalities in the prefrontal cortex of schizophrenia and other psychiatric disorders shed new light on these cells. We have obtained the genetic signature of perineuronal oligodendrocytes by identifying gene expression differences between oligodendrocyte subpopulations using cell-specific tags, microarray technology, quantitative time-resolved polymerase chain reaction and bioinformatics tools. We show that perineuronal cells are the progeny of oligodendrocyte progenitors and, hence, are members of the oligodendrocyte lineage. Physiologically they exhibit a novel phenotype. Their expression of PDGFR-?? and its growth factor ligand PDGF-CC sets them apart from members of their lineage as this receptor precludes their response to the same growth factors that act on myelinating cells. Their coordinate expression and context-specific usage of transcription factors Olig2, Ascl1 and Pax6, together with the prominent presence of transcription factors Pea3, Lhx2 and Otx2 – not hitherto linked to the oligodendrocyte lineage – suggested a cell with features that blur the boundary between a neuron and a glial cell. But they also maintain a reservoir of untranslated transcripts encoding major myelin proteins presumably for a demyelinating episode. This first molecular characterization of perineuronal oligodendrocytes revealed the striking difference between the myelinating and non-myelinating phenotypes. PMID:22132705

Szuchet, Sara; Nielsen, Joseph A.; Lovas, Gabor; Domowicz, Miriam S.; de Velasco, Javier M.; Maric, Dragan; Hudson, Lynn D.

2014-01-01

73

Development and genetic mapping of SSR markers in foxtail millet [ Setaria italica (L.) P. Beauv.  

Microsoft Academic Search

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In\\u000a this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected

Xiaoping Jia; Zhongbao Zhang; Yinghui Liu; Chengwei Zhang; Yunsu Shi; Yanchun Song; Tianyu Wang; Yu Li

2009-01-01

74

Gold fiducials are a unique marker for localization in the thoracic spine: a cost comparison with percutaneous vertebroplasty.  

PubMed

We present a unique application of the gold fiducial as a preoperative, radiographic marker placed in the thoracic spine and used for intraoperative localization. In comparison to percutaneous vertebroplasty marking of thoracic spinal levels with polymethyl methacrylate (PMMA) cement, implantation of the gold fiducial is technically facile with a minimal learning curve. The fiducial markers are also associated with significantly less financial resources. Following 2013 Current Procedural Terminology (CPT) coding, the cost of vertebroplasty under fluoroscopic guidance, $3195·43, or under computed tomography (CT) guidance, $3232·54, is more than double the cost of the gold fiducial implantation - $1237·55 and $1267·03, under similar imaging techniques, respectively. In the first description of gold fiducials in the thoracic spine, we conclude that the marker is a safe and cost-effective method for preoperative localization of the thoracic levels. PMID:24963696

Macki, Mohamed; Bydon, Mohamad; McGovern, Kelly; Abt, Nicholas; de la Garza-Ramos, Rafael; Naff, Neal; Bydon, Ali

2014-10-01

75

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants  

PubMed Central

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-01-01

76

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.  

PubMed

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-09-01

77

Assessment of diversity in Podophyllum hexandrum by genetic and phytochemical markers  

Microsoft Academic Search

For successful conservation and domestication of a species, evaluation of its genetic diversity by different markers is important. Morphological characteristics, phytochemical variation and random amplified polymorphic DNA (RAPD) profiles were generated in different accessions of Podophyllum hexandrum in order to determine the genetic diversity. Random amplified polymorphic DNA (RAPD) analysis revealed a high degree of genetic diversity among the accessions

P. Sultan; A. S. Shawl; P. W. Ramteke; A. Kour; P. H. Qazi

2008-01-01

78

A Study of Conservation Genetics in Cupressus chengiana , an Endangered Endemic of China, Using ISSR Markers  

Microsoft Academic Search

ISSR markers were used to analyze the genetic diversity and genetic structure of eight natural populations of Cupressus chengiana in China. ISSR analysis using 10 primers was carried out on 92 different samples. At the species level, 136 polymorphic loci were detected. The percentage of polymorphic bands (PPB) was 99%. Genetic diversity (H e) was 0.3120, effective number of alleles

Bingqing Hao; Wang Li; Mu Linchun; Yao Li; Zhang Rui; Tang Mingxia; Bao Weikai

2006-01-01

79

Marker based estimates of between and within population kinships for the conservation of genetic diversity  

Microsoft Academic Search

Summary In this article coefficients of kinship between and within populations are proposed as a tool to assess genetic diversity for conservation of genetic variation. However, pedigree-based kinships are often not available, especially between populations. A method of estimation of kinship from genetic marker data was applied to simulated data from random breeding populations in order to study the suitability

H. Eding; T. H. E. Meuwissen

2001-01-01

80

Genetic diversity within and between European pig breeds using microsatellite markers  

Microsoft Academic Search

An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds,

M. SanCristobal; C. Chevalet; C. S. Haley; R. Joosten; A. P. Rattink; B. Harlizius; M. A. M. Groenen; Y. Amigues; M.-Y. Boscher; G. Russell; A. Law; R. Davoli; V. Russo; C. Desautes; L. Alderson; E. Fimland; M. Bagga; J. V. Delgado; J. L. Vega-Pla; A. M. Martinez; M. Ramos; P. Glodek; J. N. Meyer; G. C. Gandini; D. Matassino; G. S. Plastow; K. W. Siggens; G. Laval; A. L. Archibald; D. Milan; K. Hammond; R. Cardellino

2006-01-01

81

Molecular markers, genetic maps, and QTLs for peanut molecular breeding in peanut  

Technology Transfer Automated Retrieval System (TEKTRAN)

Integration of plant breeding, genetics and genomics promises to foster genetic enhancement leading to increased productivity, oil quality and resistance/tolerance to biotic and abiotic stresses. Recent advances have resulted in the development of genomic resources such as SSR markers, and genetic m...

82

Autism and genetics: Clinical approach and association study with two markers of HRAS gene  

SciTech Connect

Twin studies and familial aggregation studies indicate that genetic factors could play a role in infantile autism. In an earlier study, we identified a possible positive association between autism and a c-Harvey-ras (HRAS) oncogene marker at the 3{prime} end of the coding region. In an attempt to confirm this finding, we studied a larger population, well-characterized clinically and genetically. We report a positive association between autism and two HRAS markers, the 3{prime} marker used in the initial study and an additional marker in exon 1. 46 refs., 1 fig., 2 tabs.

Herault, J.; Petit, E.; Cherpi, C. [Laboratoire de Biochimie Medicale, Tours (France)] [and others

1995-08-14

83

Alu repeats as markers for human population genetics  

SciTech Connect

The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Bazan, H. [Louisiana State Univ., New Orleans, LA (United States). Medical Center] [and others

1993-09-01

84

Genetic assessment of safflower (Carthamus tinctorius L.) collection with microsatellite markers acquired via pyrosequencing method.  

PubMed

A genetic evaluation of safflower germplasm collections derived from different geographical regions and countries will provide useful information for sustainable conservation and the utilization of genetic diversity. However, the molecular marker information is limited for evaluation of genetic diversity of safflower germplasm. In this study, we acquired 509 putative genomic SSR markers for sufficient genome coverage using next-generation sequencing methods and characterized thirty polymorphic SSRs in safflower collection composed of 100 diverse accessions. The average allele number and expected heterozygosity were 2.8 and 0.386, respectively. Analysis of population structure and phylogeny based on thirty SSR profiles revealed genetic admixture between geographical regions contrary to genetic clustering. However, the accessions from Korea were genetically conserved in distinctive groups in contrast to other safflower gene pool. In conclusion, these new genomic SSRs will facilitate valuable studies to clarify genetic relationships as well as conduct population structure analyses, genetic map construction and association analysis for safflower. PMID:23875976

Lee, Gi-An; Sung, Jung-Sook; Lee, Sok-Young; Chung, Jong-Wook; Yi, Jung-Yoon; Kim, Yeon-Gyu; Lee, Myung-Chul

2014-01-01

85

Complete Nucleotide Sequence of a Citrobacter freundii Plasmid Carrying KPC-2 in a Unique Genetic Environment  

PubMed Central

The complete and annotated nucleotide sequence of a 54,036-bp plasmid harboring a blaKPC-2 gene that is clonally present in Citrobacter isolates from different species is presented. The plasmid belongs to incompatibility group N (IncN) and harbors the class A carbapenemase KPC-2 in a unique genetic environment. PMID:25395635

Yao, Yancheng; Imirzalioglu, Can; Hain, Torsten; Kaase, Martin; Gatermann, Soeren; Exner, Martin; Mielke, Martin; Hauri, Anja; Dragneva, Yolanta; Bill, Rita; Wendt, Constanze; Wirtz, Angela; Chakraborty, Trinad

2014-01-01

86

Complete Nucleotide Sequence of a Citrobacter freundii Plasmid Carrying KPC-2 in a Unique Genetic Environment.  

PubMed

The complete and annotated nucleotide sequence of a 54,036-bp plasmid harboring a blaKPC-2 gene that is clonally present in Citrobacter isolates from different species is presented. The plasmid belongs to incompatibility group N (IncN) and harbors the class A carbapenemase KPC-2 in a unique genetic environment. PMID:25395635

Yao, Yancheng; Imirzalioglu, Can; Hain, Torsten; Kaase, Martin; Gatermann, Soeren; Exner, Martin; Mielke, Martin; Hauri, Anja; Dragneva, Yolanta; Bill, Rita; Wendt, Constanze; Wirtz, Angela; Domann, Eugen; Chakraborty, Trinad

2014-01-01

87

Determination of a Unique Solution to Parallel Proton Transfer Reactions Using the Genetic Algorithm  

E-print Network

Determination of a Unique Solution to Parallel Proton Transfer Reactions Using the Genetic proton transfer reactions to rigorous kinetic analysis, which consists of solving a set of coupled of Mathematics, The Faculty of Exact Sciences, and y Laser Laboratory for Fast Reactions in Biology, Department

Fibich, Gadi

88

Psychological aspects of human cloning and genetic manipulation: the identity and uniqueness of human beings  

Microsoft Academic Search

Human cloning has become one of the most controversial debates about reproduction in Western civilization. Human cloning represents asexual reproduction, but the critics of human cloning argue that the result of cloning is not a new individual who is genetically unique. There is also awareness in the scientific community, including the medical community, that human cloning and the creation of

NM Morales

2009-01-01

89

[Relationship of the course of nephrotuberculosis in patients to various combinations of genetic markers].  

PubMed

To examine the body's responsiveness in different forms of nepthrotuberculosis, 237 patients underwent comprehensive clinical laboratory studies. To reveal various combinations of genetic markers, the authors determine the phenotypes of haptoglobin, the activity of red blood cell glucose-6-phosphate dehydrogenase, the type of inactivation of isonicotinic acid hydrazide. According to the combinations of a complex of these genetic markers, the authors identified 4 combinations: poor, good, relatively poor, and relatively good. The studies indicated the high incidence of common forms of nephrotuberculosis in subjects with poor and relatively poor combinations of genetic markers. The determination of various chronic renal failure-associated combinations of genetic markers may be used to identify risk groups for this disease. PMID:18080530

Khakimov, M A; Uba?dullaev, A M; Kazakov, K S

2007-01-01

90

Marker-assisted estimation of quantitative genetic parameters in rainbow trout, Oncorhynchus mykiss  

E-print Network

Marker-assisted estimation of quantitative genetic parameters in rainbow trout, Oncorhynchus mykiss in an aquaculture population of rainbow trout (Oncorhynchus mykiss). Firstly a regression-based model employing

Wilson, Alastair

91

Characterization of the genetic resources of redcurrant (Ribes rubrum: subg. Ribesia) using anchored microsatellite markers  

Microsoft Academic Search

Redcurrant, Ribes rubrum L., germplasm was screened for molecular polymorphism using anchored microsatellite primers in polymerase chain reactions\\u000a (PCRs). Eighty markers were detected using only three primers and 16 redcurrant genotypes were fingerprinted using these markers.\\u000a The genetic relatedness of these genotypes, as determined by the anchored microsatellite markers, and the implications for\\u000a redcurrant breeding programmes are examined.

P. G. Lanham; R. M. Brennan

1998-01-01

92

A genetic map of Maritime pine based on AFLP, RAPD and protein markers  

Microsoft Academic Search

TheAFLP (amplified fragment length polymorphism) technique was adapted to carry out genetic analysis in maritime pine, a species\\u000a characterized by a large genome size (24 pg\\/C). A genetic linkage map was constructed for one F1 individual based on 239 AFLP and 127 RAPD (randomly amplified polymorphic DNA) markers. Markers were scored on megagametophytes\\u000a (1n) from 200 germinated F2 seedlings. Polymorphism

P. Costa; D. Pot; C. Dubos; J. M. Frigerio; C. Pionneau; C. Bodenes; E. Bertocchi; M.-T. Cervera; D. L. Remington; C. Plomion

2000-01-01

93

Genetic Divergence Detected by ISSR Markers and Characterization of Microsatellite Regions in Mytilus Mussels  

Microsoft Academic Search

The wide distribution of microsatellites in mussels of the Mytilus edulis complex (Mytilidae) enables the analysis of inter-simple-sequence repeat (ISSR) markers. The aim of this investigation was\\u000a to assess genetic differentiation in six sampling localities distributed along the European Atlantic coast to expose the potential\\u000a of these markers in genetic studies requiring the detection of low polymorphism and as a

Miguel A. Varela; Ana González-Tizón; Luis Mariñas; Andrés Martínez-Lage

2007-01-01

94

Cystic Fibrosis Locus Defined by a Genetically Linked Polymorphic DNA Marker  

Microsoft Academic Search

A polymorphic DNA marker has been found genetically linked, in a set of 39 human families, to an autosomal recessive gene that causes cystic fibrosis (CF), a disease affecting one in 2000 Caucasian children. The DNA marker (called D0CRI-917) is also linked to the PON locus, which by independent evidence is linked to the CF locus. The best estimates of

Lap-Chee Tsui; Manuel Buchwald; David Barker; Jeffrey C. Braman; Robert Knowlton; James W. Schumm; Hans Eiberg; Jan Mohr; Dara Kennedy; Natasa Plavsic; Martha Zsiga; Danuta Markiewicz; Gita Akots; Valerie Brown; Cynthia Helms; Thomas Gravius; Carol Parker; Kenneth Rediker; Helen Donis-Keller

1985-01-01

95

Assessing genetic diversity of wheat ( Triticum aestivum L.) germplasm using microsatellite markers  

Microsoft Academic Search

A set of 24 wheat microsatellite markers, representing at least one marker from each chromosome, was used for the assessment of genetic diversity in 998 accessions of hexaploid bread wheat (Triticum aestivum L.) which originated from 68 countries of five continents. A total of 470 alleles were detected with an average allele number of 18.1 per locus. The highest number

X. Q. Huang; A. Börner; M. S. Röder; M. W. Ganal

2002-01-01

96

An efficient method to find potentially universal population genetic markers, applied to metazoans  

Microsoft Academic Search

BACKGROUND: Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron

Anne Chenuil; Thierry B Hoareau; Emilie Egea; Gwilherm Penant; Caroline Rocher; Didier Aurelle; Kenza Mokhtar-Jamai; John DD Bishop; Emilie Boissin; Angie Diaz; Manuela Krakau; Pieternella C Luttikhuizen; Francesco P Patti; Nicolas Blavet; Sylvain Mousset

2010-01-01

97

A genetic linkage map of papaya based on randomly amplified polymorphic DNA markers  

Microsoft Academic Search

A genetic linkage map of papaya (Carica papaya L.) was constructed using randomly amplified polymorphic DNA (RAPD) markers and a F2 population derived from a University of Hawaii UH breeding line 356 x ‘Sunrise’ cross. A total of 596 10-mer primers were screened, and 96 polymorphisms were detected. At LOD 4.0, 62 of these markers mapped to 11 linkage groups

S. N. Sondur; R. M. Manshardt; J. I. Stiles

1996-01-01

98

Usefulness of WRKY gene-derived markers for assessing genetic diversity of Florida coconut cultivars  

Technology Transfer Automated Retrieval System (TEKTRAN)

Analysis of the genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm representing eight cultivars was previously described using 15 microsatellite (simple sequence repeat, SSR) markers. Here we report on the analysis of the same genotypes using 13 markers d...

99

Genetic analysis of the fragile-X mental retardation syndrome with two flanking polymorphic DNA markers  

SciTech Connect

The fragile-X mental retardation syndrome, one of the most prevalent chromosome X-linked diseases (approx. = 1 of 2000 newborn males), is characterized by the presence in affected males and in a portion of carrier females of a fragile site at chromosome band Xq27. The authors have performed a linkage analysis in 16 families between the locus for the fragile-X syndrome, FRAXQ27, and two polymorphic DNA markers that correspond to the anonymous probe St14 and to the coagulation factor IX gene F9. The results indicate that the order of loci is centromere-F9-FRAXQ27-St14-Xqter. The estimate of the recombination fraction for the linkage F9-FRAXQ27 is 0.12 and 0.10 for FRAXQ27-St14. Recombination between St14 and F9 does not appear to be significantly different in normal and fragile-X families. The two flanking probes were used for diagnosis of the carrier state and for detection of transmission of the disease through phenotypically normal males. They should also allow first-trimester diagnosis with a reliability of about 98% in 40% of the families. Used in conjunction with the cytogenetic analysis, the segregation studies with both probes should improve the genetic counseling for the fragile-X syndrome and should be useful for the formal genetic analysis of this unique disease.

Oberle, I.; Heilig, R.; Moisan, J.P.; Kloepfer, C.; Mattei, M.G.; Mattei, J.F.; Boue, J.; Froster-Iskenius, U.; Jacobs, P.A.; Lathrop, G.M.; Lalouel, J.M.

1986-02-01

100

Distribution of Genetic Marker Concentrations for Fecal Indicator Bacteria in Sewage and Animal Feces  

PubMed Central

Very little is known about the density and distribution of fecal indicator bacteria (FIB) genetic markers measured by quantitative real-time PCR (qPCR) in fecal pollution sources. Before qPCR-based FIB technologies can be applied to waste management and public health risk applications, it is vital to characterize the concentrations of these genetic markers in pollution sources (i.e., untreated wastewater and animal feces). We report the distribution of rRNA genetic markers for several general FIB groups, including Clostridium spp., Escherichia coli, enterococci, and Bacteroidales, as determined by qPCR on reference collections consisting of 54 primary influent sewage samples collected from treatment facilities across the United States and fecal samples representing 20 different animal species. Based on raw sewage sample collection data, individual FIB genetic markers exhibited a remarkable similarity in concentration estimates from locations across the United States ranging from Hawaii to Florida. However, there was no significant correlation between genetic markers for most FIB combinations (P > 0.05). In addition, large differences (up to 5 log10 copies) in the abundance of FIB genetic markers were observed between animal species, emphasizing the importance of indicator microorganism selection and animal source contribution for future FIB applications. PMID:22504809

Kelty, Catherine A.; Varma, Manju; Sivaganesan, Mano; Haugland, Richard A.

2012-01-01

101

Decay of genetic markers for fecal bacterial indicators and pathogens in sand from Lake Superior.  

PubMed

Beach sands impact water quality and pathogen loads, however, the comparative decay of the fecal indicator bacteria (FIB) Enterococcus spp. and Escherichia coli, and pathogens in freshwater sand have not been examined. In this study, freshwater sand microcosms were inoculated with sewage and pure cultures of bacterial pathogens to compare relative decay rates. The abundance of culturable Enterococcus spp. and E. coli, genetic markers for Enterococcus spp. (Entero1), total Bacteroides (AllBac), and human-specific Bacteroides (HF183), and genetic markers for the pathogens Campylobacter jejuni, methicillin-resistant Staphylococcus aureus (MRSA), Salmonella enterica subsp. enterica serovar Typhimurium, and Shigella flexneri were monitored over the course of two weeks using conventional culture methods and quantitative PCR (qPCR). The effect of moisture on the persistence of culturable FIB and all genetic markers was also determined. In addition, propidium monoazide (PMA) treatment was used to examine differences in the persistence of total genetic markers and those from live cells. Decay rates were statistically compared using Tukey's test. Moisture had a significant (p ? 0.05) effect on the decay rates of culturable indicator bacteria, total AllBac markers, and genetic markers for FIB, Salmonella, and MRSA from live cells. At 14% sand moisture, the decay rate of total markers was slower than that of live cells for all qPCR assays, but at 28% moisture, there was no difference in the decay rates of total and live markers for any assay. AllBac and MRSA markers increased in sand at 28% moisture, probably indicating cellular growth. Overall, culturable FIB and HF183 had decay rates that were most comparable to the bacterial pathogen markers examined in this study, whereas Entero1 and AllBac rarely exhibited decay rates similar to the bacterial pathogens in this study. The choice of FIB for assessment of fecal contamination in freshwater sand should take into account the pathogen of concern and sand moisture conditions. PMID:24793108

Eichmiller, Jessica J; Borchert, Andrew J; Sadowsky, Michael J; Hicks, Randall E

2014-08-01

102

Genetic markers reveal novel genes which control rice cooking quality  

Technology Transfer Automated Retrieval System (TEKTRAN)

Rice molecular markers have been developed in the gene (Waxy) that controls grain amylose content and the gene (Alk) that controls alkali spreading value. Both of these factors are considered the major determinants of rice cooking quality and texture. This set of markers is now being routinely used...

103

Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.].  

PubMed

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F(2) population, i.e. "B100" of cultivated S. italica and "A10" of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces' grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together. PMID:19139840

Jia, Xiaoping; Zhang, Zhongbao; Liu, Yinghui; Zhang, Chengwei; Shi, Yunsu; Song, Yanchun; Wang, Tianyu; Li, Yu

2009-02-01

104

An annotated genetic map of loblolly pine based on microsatellite and cDNA markers  

PubMed Central

Background Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda. PMID:21269494

2011-01-01

105

The Genetic Structure of the Kuwaiti Population: Mitochondrial DNA Markers  

E-print Network

the expansion of early Homo sapiens out of Africa. Kuwait is located in the Northeast portion of the Arabian Peninsula. This thesis investigated the mitochondrial DNA (mtDNA) genetic variation in 117 unrelated individuals to determine the genetic structure...

Theyab, Jasem

2010-06-14

106

Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers  

PubMed Central

Background Field pea (Pisum sativum L.) and faba bean (Vicia faba L.) are cool-season grain legume species that provide rich sources of food for humans and fodder for livestock. To date, both species have been relative 'genomic orphans' due to limited availability of genetic and genomic information. A significant enrichment of genomic resources is consequently required in order to understand the genetic architecture of important agronomic traits, and to support germplasm enhancement, genetic diversity, population structure and demographic studies. Results cDNA samples obtained from various tissue types of specific field pea and faba bean genotypes were sequenced using 454 Roche GS FLX Titanium technology. A total of 720,324 and 304,680 reads for field pea and faba bean, respectively, were de novo assembled to generate sets of 70,682 and 60,440 unigenes. Consensus sequences were compared against the genome of the model legume species Medicago truncatula Gaertn., as well as that of the more distantly related, but better-characterised genome of Arabidopsis thaliana L.. In comparison to M. truncatula coding sequences, 11,737 and 10,179 unique hits were obtained from field pea and faba bean. Totals of 22,057 field pea and 18,052 faba bean unigenes were subsequently annotated from GenBank. Comparison to the genome of soybean (Glycine max L.) resulted in 19,451 unique hits for field pea and 16,497 unique hits for faba bean, corresponding to c. 35% and 30% of the known gene space, respectively. Simple sequence repeat (SSR)-containing expressed sequence tags (ESTs) were identified from consensus sequences, and totals of 2,397 and 802 primer pairs were designed for field pea and faba bean. Subsets of 96 EST-SSR markers were screened for validation across modest panels of field pea and faba bean cultivars, as well as related non-domesticated species. For field pea, 86 primer pairs successfully obtained amplification products from one or more template genotypes, of which 59% revealed polymorphism between 6 genotypes. In the case of faba bean, 81 primer pairs displayed successful amplification, of which 48% detected polymorphism. Conclusions The generation of EST datasets for field pea and faba bean has permitted effective unigene identification and functional sequence annotation. EST-SSR loci were detected at incidences of 14-17%, permitting design of comprehensive sets of primer pairs. The subsets from these primer pairs proved highly useful for polymorphism detection within Pisum and Vicia germplasm. PMID:22433453

2012-01-01

107

Genetic diversity in European winter triticale determined with SSR markers and coancestry coefficient  

Microsoft Academic Search

Knowledge of the genetic diversity of a species is important for the choice of crossing parents in line and hybrid breeding. Our objective was to investigate European winter triticale using simple sequence repeat (SSR) markers and the coancestry coefficient (f) with regard to genetic diversity and grouping of germplasm. Three to five primer pairs for each of the 42 chromosomes

S. H. Tams; E. Bauer; G. Oettler; A. E. Melchinger

2004-01-01

108

Developing AFLP Markers to study genetic differentiation of the Cotton Fleahopper, Pseudatomoscelis seriatus (Reuter) (Hemiptera: Miridae)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genetic comparisons of fleahopper populations in cotton and weed hosts may be useful for identifying the weed sources contributing the majority of fleahoppers in cotton. Molecular markers such as amplified fragment length polymorphisms (AFLP) are useful to identify genetic similarities and differen...

109

Influence of wastewater disinfection on densities of culturable fecal indicator bacteria and genetic markers.  

PubMed

The US Environmental Protection Agency has proposed the use of quantitative polymerase chain reaction (qPCR) as a rapid alternative analytical method for monitoring recreational water quality at beaches. For qPCR to be considered for other Clean Water Act purposes, such as inclusion in discharge permits and use in Total Maximum Daily Load calculations, it is necessary to understand how qPCR detectable genetic markers are influenced by wastewater disinfection. This study investigated genetic markers for Escherichia coli, Enterococcus, Clostridium spp., Bacteroides, total Bacteroidales, as well as the human-associated Bacteroides markers, HF183 and HumM2, to determine which, if any, were influenced by disinfection (chlorination or ultraviolet light) of effluents from secondary wastewater treatment in different seasons. The effects of disinfection on culturable enterococci, E. coli, Bacteroides, and C. perfringens were also compared to their associated genetic markers. Disinfection of secondary treatment effluents significantly reduced culturable fecal indicator bacteria (FIB) but not genetic marker densities. No significant differences were observed in the responses of FIB culture and genetic marker densities to type of disinfection (chlorination vs UV) or season. Results of this study provide evidence that qPCR may not be suitable for monitoring efficacy of wastewater disinfection on the inactivation of bacterial pathogens. PMID:25252344

Chern, Eunice C; Brenner, Kristen; Wymer, Larry; Haugland, Richard A

2014-09-01

110

A novel set of single-copy nuclear DNA markers for the genetic study of Salicaceae.  

PubMed

Species of Populus are widely distributed worldwide, playing a significant role in both ecology and economy. However, the lack of single-copy nuclear markers limits knowledge about the phylogeny and population genetics of this genus. In the present study, primer pairs of 15 single-copy nuclear markers were developed through bioinformatic methods based on complete genomic sequences of Populus trichocarpa and Salix arbutifolia. Twenty individuals of Populus davidiana Dode and Salix matsudana Koidz were used to evaluate the basic application of these markers with respect to marker length and diversity indices, respectively. The utility of single-copy nuclear markers is anticipated to facilitate further studies about the phylogeny, population genetics, and phylogeography of this genus, in addition to providing information about the evolutionary dynamics of Salicaceae. PMID:25062424

Du, S H; Wang, Z S; Zhang, J G

2014-01-01

111

Recent Patents on Biosafety Strategies of Selectable Marker Genes in Genetically Modified Crops.  

PubMed

Genetically modified crops (GMCs) have been planted world wide since 1990, but the potential insecurity of selectable marker genes raises the questions about GMC safety. Therefore, several researches have been conducted on marker gene safety issues and several patents have been issued on this subject recently. There are two main approaches to achieve this goal: seeking the biosafety selectable marker and eliminating these insecure marker genes after transformation. Results show that these two systems are quite effective. Recent patents on the two ways are discussed in this review. PMID:25342150

Jiang, Yiming; Hu, Xiaoning; Huang, Haiying

2014-10-23

112

Genetic Biodiversity of Italian Olives (Olea europaea) Germplasm Analyzed by SSR Markers  

PubMed Central

The olive is an important fruit species cultivated for oil and table olives in Italy and the Mediterranean basin. The conservation of cultivated plants in ex situ collections is essential for the optimal management and use of their genetic resources. The largest ex situ olive germplasm collection consists of approximately 500 Italian olive varieties and corresponding to 85% of the total Italian olive germplasm is maintained at the Consiglio per la Ricerca e sperimentazione per l'Agricoltura, Centro di Ricerca per l'Olivicoltura e l'Industria Olearia (CRA-OLI), in Italy. In this work, eleven preselected nuclear microsatellite markers were used to assess genetic diversity, population structure, and gene flows with the aim of assembling a core collection. The dendrogram obtained utilizing the unweighted pair group method highlights the presence of homonymy and synonymy in olive tree datasets analyzed in this study. 439 different unique genotype profiles were obtained with this combination of 11 loci nSSR, representing 89.8% of the varieties analyzed. The remaining 10.2% comprises different variety pairs in which both accessions are genetically indistinguishable. Clustering analysis performed using BAPS software detected seven groups in Italian olive germplasm and gene flows were determined among identified clusters. We proposed an Italian core collection of 23 olive varieties capturing all detected alleles at microsatellites. The information collected in this study regarding the CRA-OLI ex situ collection can be used for breeding programs, for germplasm conservation, and for optimizing a strategy for the management of olive gene pools. PMID:24723801

Vendramin, Giuseppe Giovanni; Chiappetta, Adriana

2014-01-01

113

Potential of marker-assisted selection in hemp genetic improvement  

Microsoft Academic Search

Summary  The development and applications of molecular markers to hemp breeding are recent, dating back only to the mid-1990s. The main achievements in this field are reviewed. The analysis of Cannabis germplasm by RAPD, AFLP and microsatellites is discussed, with its consequence for the still debated species concept in Cannabis. DNA-based markers have also been exploited in the field of forensic

G. Mandolino; A. Carboni

2004-01-01

114

Psychological aspects of human cloning and genetic manipulation: the identity and uniqueness of human beings.  

PubMed

Human cloning has become one of the most controversial debates about reproduction in Western civilization. Human cloning represents asexual reproduction, but the critics of human cloning argue that the result of cloning is not a new individual who is genetically unique. There is also awareness in the scientific community, including the medical community, that human cloning and the creation of clones are inevitable. Psychology and other social sciences, together with the natural sciences, will need to find ways to help the healthcare system, to be prepared to face the new challenges introduced by the techniques of human cloning. One of those challenges is to help the healthcare system to find specific standards of behaviour that could be used to help potential parents to interact properly with cloned babies or children created through genetic manipulation. In this paper, the concepts of personality, identity and uniqueness are discussed in relationship to the contribution of twin studies in these areas. The author argues that an individual created by human cloning techniques or any other type of genetic manipulation will not show the donor's characteristics to the extent of compromising uniqueness. Therefore, claims to such an effect are needlessly alarmist. PMID:19891847

Morales, N M

2009-01-01

115

The origin of the Japanese race based on genetic markers of immunoglobulin G  

PubMed Central

This review addresses the distribution of genetic markers of immunoglobulin G (Gm) among 130 Mongoloid populations in the world. These markers allowed the populations to be clearly divided into 2 groups, the northern and southern groups. The northern group is characterized by high frequencies of 2 marker genes, ag and ab3st, and an extremely low frequency of the marker gene afb1b3; and the southern group, in contrast, is indicated by a remarkably high frequency of afb1b3 and low frequencies of ag and ab3st. Based on the geographical distribution of the markers and gene flow of Gm ag and ab3st (northern Mongoloid marker genes) from northeast Asia to the Japanese archipelago, the Japanese population belongs basically to the northern Mongoloid group and is thus suggested to have originated in northeast Asia, most likely in the Baikal area of Siberia. PMID:19212099

Matsumoto, Hideo

2009-01-01

116

Levels of genetic polymorphism: marker loci versus quantitative traits.  

PubMed Central

Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species. PMID:9533123

Butlin, R K; Tregenza, T

1998-01-01

117

Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects  

PubMed Central

Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

Malik, Waqas; Iqbal, Muhammad Zaffar; Ali Khan, Asif; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Qadir Ahmad, Muhammad; Hasan Abbasi, Ghulam

2014-01-01

118

Evaluation of genetic variability, rust resistance and marker-detection in cultivated Artemisia dracunculus from Iran.  

PubMed

Artemisia dracunculus L. (tarragon), a small shrubby perennial herb, is cultivated for the use of its aromatic leaves in seasoning, salads, etc., and in the preparation of tarragon vinegar. In the present work, genetic analysis of 29 cultivated individuals of this species was carried out employing 12 ISSR and 11 SRAP markers. A total of 59 (71.64%) and 79 (83.14%) polymorphic bands were detected by 12 ISSR primers and 11 SRAP primer pairs, respectively. High similarity for patterns of genetic diversity and clustering of individuals was observed using two ISSR and SRAP marker systems and combined data. Range of genetic similarity by ISSR markers was 0.14 to 0.95, by SRAP markers was 0.14 to 0.90, while this range varied from 0.18 to 0.91 by ISSR+SRAP. In the UPGMA cluster analysis (ISSR, SRAP and ISSR+SRAP), we always found two clusters, the first cluster included 22 individuals and the second contained seven individuals. The results demonstrated that both ISSR and SRAP methods were suitable for discriminating among the studied individuals and the SRAP markers were more efficient and preferable. The results of multiple regression analysis revealed statistically significant association between rust resistance and some molecular markers that they can provide clues for identification of the individuals with higher rust resistance. The molecular marker-based study of genetic diversity suggests that the germplasm studied representing the kind of variability would be a valuable genetic resource for future breeding. In addition, in situ conservation measures are recommended to preserve the valuable A. dracunculus genetic resources as the most effective and economical approach. PMID:25445292

Karimi, Ali; Hadian, Javad; Farzaneh, Mohsen; Khadivi-Khub, Abdollah

2015-01-10

119

Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat  

PubMed Central

Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity. PMID:23538839

Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M.; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

2013-01-01

120

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis  

PubMed Central

The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove). PMID:22422763

Bryant, David; Bouckaert, Remco; Felsenstein, Joseph; Rosenberg, Noah A.; RoyChoudhury, Arindam

2012-01-01

121

Augmenting the Genetic Toolbox for Sulfolobus islandicus with a Stringent Positive Selectable Marker for Agmatine Prototrophy  

PubMed Central

Sulfolobus species have become the model organisms for studying the unique biology of the crenarchaeal division of the archaeal domain. In particular, Sulfolobus islandicus provides a powerful opportunity to explore natural variation via experimental functional genomics. To support these efforts, we further expanded genetic tools for S. islandicus by developing a stringent positive selection for agmatine prototrophs in strains in which the argD gene, encoding arginine decarboxylase, has been deleted. Strains with deletions in argD were shown to be auxotrophic for agmatine even in nutrient-rich medium, but growth could be restored by either supplementation of exogenous agmatine or reintroduction of a functional copy of the argD gene from S. solfataricus P2 into the ?argD host. Using this stringent selection, a robust targeted gene knockout system was established via an improved next generation of the MID (marker insertion and unmarked target gene deletion) method. Application of this novel system was validated by targeted knockout of the upsEF genes involved in UV-inducible cell aggregation formation. PMID:23835176

Cooper, Tara E.; Krause, David J.

2013-01-01

122

GENETIC MAPPING OF MAIZE MUTANTS WITH SSR MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Mapping of mutants in the Maize Mapping Project seeks to increase the value of the mutant resource with map information. Because the number of mutants is enormous, and is ever growing, we have worked to increase the rate and resolution by which mutants can be mapped with molecular markers. By prod...

123

Breakpoint analysis: Precise localization of genetic markers by means of nonstatistical computation using relatively few genotypes  

SciTech Connect

Placing new markers on a previously existing genetic map by using conventional methods of multilocus linkage analysis requires that a large number of reference families be genotyped. This paper presents a methodology for placing new markers on existing genetic maps by genotyping only a few individuals in a selected subset of the reference panel. We show that by identifying meiotic breakpoint events within existing genetic maps and genotyping individuals who exhibit these events, along with one nonrecombinant sibling and their parents, we can determine precise locations for new markers even within subcentimorgan chromosomal regions. This method also improves detection of errors in genotyping and assists in the observation of chromosome behavior in specific regions. 31 refs., 9 figs.

Elsner, T.I.; Albertsen, H.; Gerken, S.C.; Cartwright, P.; White, R. [Univ. of Utah, Salt Lake City, UT (United States)

1995-02-01

124

Breakpoint analysis: precise localization of genetic markers by means of nonstatistical computation using relatively few genotypes.  

PubMed Central

Placing new markers on a previously existing genetic map by using conventional methods of multilocus linkage analysis requires that a large number of reference families be genotyped. This paper presents a methodology for placing new markers on existing genetic maps by genotyping only a few individuals in a selected subset of the reference panel. We show that by identifying meiotic breakpoint events within existing genetic maps and genotyping individuals who exhibit these events, along with one nonrecombinant sibling and their parents, we can determine precise location for new markers even within subcentimorgan chromosomal regions. This method also improves detection of errors in genotyping and assists in the observation of chromosome behavior in specific regions. PMID:7847386

Elsner, T I; Albertsen, H; Gerken, S C; Cartwright, P; White, R

1995-01-01

125

Use of Three Different Marker Systems to Estimate Genetic Diversity of Indian Elite Rice Varieties  

Microsoft Academic Search

Genetic diversity among 42 Indian elite rice varieties, which is important for selection of parents for conventional breeding\\u000a and hybrid program, was evaluated using three different types of DNA markers and parentage analysis. Random amplified polymorphic\\u000a DNA (RAPD), inter-simple sequence repeat (ISSR) and sequence tagged microsatellite site (STMS) markers resulted in mean heterozygosity\\u000a values of 0.429, 0.675 and 0.882 over

A. P. Davierwala; K. V. Chowdari; Shiv Kumar; A. P. K. Reddy; P. K. Ranjekar; V. S. Gupta

2000-01-01

126

Contrasting genetic diversity relationships are revealed in rice (Oryza sativa L.) using different marker types  

Microsoft Academic Search

Genetic variation between samples of Oryza sativa from 19 localities in Bangladesh and Bhutan was assessed using two PCR-based molecular marker systems: RAPD (random amplification of polymorphic DNA) and ISSR-PCR (inter-simple sequence repeat polymerase chain reaction). Employing RAPD, a set of 14 decanucleotides of arbitrary sequence directed the amplification of 94 reproducible marker bands, 47 (50%) of which were polymorphic.

Beverley J. Parsons; H. John Newbury; Michael T. Jackson; Brian V. Ford-Lloyd

1997-01-01

127

Genetic Analysis and Linkage Mapping in a Resource Pig Population Using Microsatellite Markers  

Microsoft Academic Search

The use of markers and linkage map construction are important for QTL mapping in pigs. In this article, the genetic characteristics were studied and the linkage map was constructed in a pig resource population including 214 individuals by typing 39 microsatellite marker loci on Sus scrofa chromosomes, SSC4, SSC6, SSC7, SSC8, and SSC13. Results indicated that the average allele number,

Jinghu Zhang; Yuanzhu Xiong; Bo Zuo; Minggang Lei; Siwen Jiang; Feng'e Li; Rong Zheng; Jialian Li

2007-01-01

128

Use of Genetic Markers to Verify the Distribution of Northern Leopard Frogs (Lithobates pipiens) and Southern Leopard Frogs (Lithobates  

E-print Network

Use of Genetic Markers to Verify the Distribution of Northern Leopard Frogs (Lithobates pipiens to address this question. KEY WORDS: Lithobates pipiens, Lithobates sphenocephalus, genetics, distribution, northern leopard frogs (Lithobates pipiens) and southern leopard frogs (L. sphenocepha- lus), have

Richter, Stephen C.

129

Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.).  

PubMed

We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines 'Lynx-037DH' and 'Monty-028DH'. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. PMID:22193366

Raman, Harsh; Raman, Rosy; Nelson, Matthew N; Aslam, M N; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A; Kilian, A; Sharpe, Andrew G; Schondelmaier, Joerg

2012-01-01

130

Finding Markers That Make a Difference: DNA Pooling and SNP-Arrays Identify Population Informative Markers for Genetic Stock Identification  

PubMed Central

Genetic stock identification (GSI) using molecular markers is an important tool for management of migratory species. Here, we tested a cost-effective alternative to individual genotyping, known as allelotyping, for identification of highly informative SNPs for accurate genetic stock identification. We estimated allele frequencies of 2880 SNPs from DNA pools of 23 Atlantic salmon populations using Illumina SNP-chip. We evaluated the performance of four common strategies (global FST, pairwise FST, Delta and outlier approach) for selection of the most informative set of SNPs and tested their effectiveness for GSI compared to random sets of SNP and microsatellite markers. For the majority of cases, SNPs selected using the outlier approach performed best followed by pairwise FST and Delta methods. Overall, the selection procedure reduced the number of SNPs required for accurate GSI by up to 53% compared with randomly chosen SNPs. However, GSI accuracy was more affected by populations in the ascertainment group rather than the ranking method itself. We demonstrated for the first time the compatibility of different large-scale SNP datasets by compiling the largest population genetic dataset for Atlantic salmon to date. Finally, we showed an excellent performance of our top SNPs on an independent set of populations covering the main European distribution range of Atlantic salmon. Taken together, we demonstrate how combination of DNA pooling and SNP arrays can be applied for conservation and management of salmonids as well as other species. PMID:24358184

Ozerov, Mikhail; Vasemägi, Anti; Wennevik, Vidar; Diaz-Fernandez, Rogelio; Kent, Matthew; Gilbey, John; Prusov, Sergey; Niemelä, Eero; Vähä, Juha-Pekka

2013-01-01

131

Genetic markers of osteoarticular disorders: facts and hopes  

PubMed Central

Osteoarthritis and osteoporosis are the two most common age-related chronic disorders of articular joints and skeleton, representing a major public health problem in most developed countries. Apart from being influenced by environmental factors, both disorders have a strong genetic component, and there is now considerable evidence from large population studies that these two disorders are inversely related. Thus, an accurate analysis of the genetic component of one of these two multifactorial diseases may provide data of interest for the other. However, the existence of confounding factors must always be borne in mind in interpreting the genetic analysis. In addition, each patient must be given an accurate clinical evaluation, including family history, history of drug treatments, lifestyle, and environment, in order to reduce the background bias. Here, we review the impact of recent work in molecular genetics suggesting that powerful molecular biology techniques will soon make possible both a rapid accumulation of data on the genetics of both disorders and the development of novel diagnostic, prognostic, and therapeutic approaches. PMID:11549368

Brandi, Maria Luisa; Gennari, Luigi; Cerinic, Marco Matucci; Becherini, Lucia; Falchetti, Alberto; Masi, Laura; Gennari, Carlo; Reginster, Jean-Yves

2001-01-01

132

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae  

PubMed Central

Background The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. Conclusions The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae. PMID:21806822

2011-01-01

133

Evolution of genetic and genomic features unique to the human lineage  

PubMed Central

Given the unprecedented tools now available for rapidly comparing genomes, the identification and study of genetic and genomic changes unique to our species has accelerated, and we are entering a golden age of human evolutionary genomics. Here we provide an overview of these efforts, highlighting important recent discoveries, examples of the different types of human-specific genomic and genetic changes identified, and salient trends such as the localization of evolutionary adaptive changes to complex loci that are highly enriched for disease associations. Lastly, we discuss the remaining challenges, such as the incomplete nature of current genome sequence assemblies, and difficulties in linking human-specific genomic changes to human-specific phenotypic traits. PMID:23154808

O’Bleness, Majesta; Searles, Veronica; Varki, Ajit; Gagneux, Pascal; Sikela, James M.

2014-01-01

134

Genetic diversity of functional food species Spinacia oleracea L. by protein markers.  

PubMed

Exploration of genetic diversity contributes primarily towards crop improvement. Spinaciaoleracea L. is a functional food species but unfortunately the genetic diversity of this vegetable is still unexplored. Therefore, this research was planned to explore the genetic diversity of S. oleracea by using morphological and protein markers. Protein profile of 25 accessions was generated on sodium dodecyl sulphate polyacrylamide gel. Total allelic variation of 27 bands was found. Out of these, 20 were polymorphic and the rest of the bands were monomorphic. Molecular weights of the bands ranged from 12.6 to 91.2 kDa. Major genetic differences were observed in accession 20541 (Peshawar) followed by 20180 (Lahore) and 19902 (AVRDC). Significant differences exist in the protein banding pattern. This variation can further be studied by advanced molecular techniques, including two-dimensional electrophoresis and DNA markers. PMID:24499432

Rashid, M; Yousaf, Z; Haider, M S; Khalid, S; Rehman, H A; Younas, A; Arif, A

2014-01-01

135

Development of a comparative genetic linkage map for Armigeres subalbatus using Aedes aegypti RFLP markers.  

PubMed

One of the causative agents of lympahtic filariasis is the nematode parasite Brugia malayi that requires a competent mosquito vector for its development and transmission. Armigeres subalbatus mosquitoes rapidly destroy invading B. malayi microfilariae via a defense response known as melanotic encapsulation. We have constructed a genetic linkage map for this mosquito species using RFLP markers from Aedes aegypti. This heterologous approach was possible because of the conserved nature of the coding sequences used as markers and provided an experimental framework to evaluate the hypothesis that linkage and gene order are conserved between these mosquito species. Of the 56 Ae. aegypti markers tested, 77% hybridize to genomic DNA digests of Ar. subalbatus under stringent conditions, with 53% of these demonstrating strain-specific polymorphisms. Twenty-six Ae. aegypti markers have been mapped using an F2- segregating Ar. subalbatus population derived from a cross of strains originating in Japan and Malaysia. Linear order of these marker loci is highly conserved between the two species. Only 1 of these markers, LF92, was not linked in the manner predicted by the Ae. aegypti map. In addition, the autosomal sex-determination locus that occurs in linkage group 1 in Ae. aegypti resides in group 3 in Ar. subalbatus. The Ar. subalbatus map provides a basic genetic context that can be utilized in further genetic studies to clarify the genetic basis of parasite resistance in this mosquito and is a necessary precursor to the identification of genome regions that carry genes that determine the encapsulation phenotype. [The composite map and sequence database information for Ae. aegypti markers can be retrieved directly from the Ae. aegypti Genome Database through the World Wide Web: http://klab.agsci.colostate.edu.] PMID:9445486

Ferdig, M T; Taft, A S; Severson, D W; Christensen, B M

1998-01-01

136

Comparing AFLP, RAPD and RFLP markers for measuring genetic diversity in melon  

Microsoft Academic Search

Three different types of molecular markers, RAPD, AFLP and RFLP were used to measure genetic diversity among six genotypes\\u000a of Cucumis melo L. Each line represented a different melon genotype: Piel de Sapo, Ogen, PI161375, PI414723, Agrestis and C105. A number\\u000a of polymorphic RAPD, AFLP and RFLP bands were scored on all materials and the genetic similarity measured. Clustering analysis

J. Garcia-Mas; M. Oliver; H. Gómez-Paniagua; M. C. de Vicente

2000-01-01

137

Development and use of microsatellite markers for genetic diversity analysis of cañahua ( Chenopodium pallidicaule Aellen)  

Microsoft Academic Search

Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritional value (high in protein\\u000a and mineral content) and ability to thrive in harsh climates make it an important regional food crop throughout the Andean\\u000a region. The objectives of this study were to develop genetic markers and to quantify genetic diversity

A. Vargas; D. B. Elzinga; J. A. Rojas-Beltran; A. Bonifacio; B. Geary; M. R. Stevens; E. N. Jellen; P. J. Maughan

2011-01-01

138

Imaging genetics of structural brain connectivity and neural integrity markers  

PubMed Central

We review studies that have used diffusion imaging (DI) and magnetic resonance spectroscopy (MRS) to investigate genetic associations. A brief description of the measures obtainable with these methods and of some methodological and interpretability limitations is given. The usefulness of DI and MRS in defining intermediate phenotypes and in demonstrating the effects of common genetic variants known to increase risk for psychiatric manifestations on anatomical and metabolic phenotypes are reviewed. The main focus is on schizophrenia where the greatest amount of data has been collected. Moreover, we present an example coming from a different approach, where the genetic alteration is known (the deletion that causes Williams syndrome) and the DI phenotype can shed new light on the function of genes affected by the mutation. We conclude that, although these are still early days of this type of research and many findings remain controversial, both techniques can significantly contribute to the understanding of genetic effects in the brain and the pathophysiology of psychiatric disorders. PMID:19932755

Marenco, Stefano; Radulescu, Eugenia

2009-01-01

139

Expanding Possibilities for Intervention against Small Ruminant Lentiviruses through Genetic Marker-Assisted Selective Breeding  

PubMed Central

Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS) has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions. PMID:23771240

White, Stephen N.; Knowles, Donald P.

2013-01-01

140

RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae).  

PubMed

For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis. PMID:22205351

Zhao, Ya-E; Wu, Li-Ping

2012-06-01

141

Genetic linkage analysis of familial amyotrophic lateral sclerosis using human chromosome 21 microsatellite DNA markers  

SciTech Connect

Amyotrophic lateral sclerosis (ALS; Lou Gehrig`s Disease) is a lethal neurodegenerative disease of upper and lower motorneurons in the brain and spinal cord. We previously reported linkage of a gene for familial ALS (FALS) to human chromosome 21 using 4 restriction fragment length polymorphism DNA markers and identified disease-associated mutations in the superoxide dismutase (SOD)-1 gene in some ALS families. We report here the genetic linkage data that led us to examine the SOD-1 gene for mutations. We also report a new microsatellite DNA marker for D21S63, derived from the cosmid PW517. Ten microsatellite DNA markers, including the new marker D21S63, were used to reinvestigate linkage of FALS to chromosome 21. Genetic linkage analysis performed with 13 ALS familes for these 10 DNA markers confirmed the presence of a FALS gene on chromosome 21. The highest total 2-point LOD score for all families was 4.33, obtained at a distance of 10 cM from the marker D21S223. For 5 ALS families linked to chromosome 21, a peak 2-point LOD score of 5.94 was obtained at the DNA marker D21S223. A multipoint score of 6.50 was obtained with the markers D21S213, D21S223, D21S167, and FALS for 5 chromosome 21-linked ALS families. The haplotypes of these families for the 10 DNA markers reveal recombination events that further refined the location of the FALS gene to a segment of approximately 5 megabases (Mb) between D21S213 and D21S219. The only characterized gene within this segment was SOD-1, the structural gene for Cu, Zn SOD. 30 refs., 4 figs., 4 tabs.

Rosen, D.R.; Sapp, P.; O`Regan, J.; McKenna-Yasek, D.; Schlumpf, K.S.; Haines, J.L.; Gusella, J.F.; Horvitz, H.R.; Brown, R.H. Jr. [Massachusetts Institute of Technology, Cambridge, MA (United States)

1994-05-15

142

Combined use of maternal, paternal and bi-parental genetic markers for the identification of wolf–dog hybrids  

Microsoft Academic Search

The identification of hybrids is often a subject of primary concern for the development of conservation and management strategies, but can be difficult when the hybridizing species are closely related and do not possess diagnostic genetic markers. However, the combined use of mitochondrial DNA (mtDNA), autosomal and Y chromosome genetic markers may allow the identification of hybrids and of the

C Vilà; C Walker; A-K Sundqvist; Ø Flagstad; Z Andersone; A Casulli; I Kojola; H Valdmann; J Halverson; H Ellegren

2003-01-01

143

The chloroplast psbK-psbI intergenic region, a potential genetic marker for broad sectional relationships in Anthurium  

Technology Transfer Automated Retrieval System (TEKTRAN)

Nuclear and chloroplast genetic markers have been extensively used for plant identification and molecular taxonomy studies. The efficacy of genetic markers to be used as DNA barcodes is under constant evaluation and improvement, with identification of new barcodes that provide greater resolution an...

144

Retene emission from residential solid fuels in China and evaluation of retene as a unique marker for soft wood combustion.  

PubMed

Retene (1-methyl-7-isopropylphenanthrene) is often used as a marker for softwood combustion and for polycyclic aromatic hydrocarbon (PAH) source apportionment. The emission factors of retene (EF(RET)s) from 11 crop residues, 27 firewood fuels, and 5 coals were measured using traditional rural Chinese stoves. Retene was measured in combustion emissions from all of the residential fuels tested and EF(RET)s varied significantly among the fuels due to the differences in fuel properties and combustion conditions. EF(RET)s for pine (0.34 ± 0.08 mg/kg) and larch (0.29 ± 0.22 mg/kg) were significantly higher than those of other wood types, including fir and cypress (0.081 ± 0.058 mg/kg). However, EF(RET)s for crop residues varied from 0.048 ± 0.008 to 0.37 ± 0.14 mg/kg and were not significantly lower than those for softwood (0.074 ± 0.026 to 0.34 ± 0.08 mg/kg). The EF(RET)s for coal were very high and ranged from 2.2 ± 1.5 (anthracite briquette) to 187 ± 113 mg/kg (raw bituminous chunk). EF(RET) was positively correlated with EFs of coemitted particulate matter (EF(PM)) and phenanthrene (EF(PHE)) for crop residue and coal, but not for wood. In addition, the ratios of EF(PHE)/EF(RET) and EF(PM)/EF(RET) for coals were much lower than those for crop residues and wood. These data suggest that retene is not a unique PAH marker for softwood combustion and that coal combustion, in particular, should be taken into account when retene is used for PAH source apportionment. PMID:22452486

Shen, Guofeng; Tao, Shu; Wei, Siye; Zhang, Yanyan; Wang, Rong; Wang, Bin; Li, Wei; Shen, Huizhong; Huang, Ye; Yang, Yifeng; Wang, Wei; Wang, Xilong; Simonich, Staci L Massey

2012-04-17

145

Markers  

ERIC Educational Resources Information Center

Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

Healthy Schools Network, Inc., 2011

2011-01-01

146

COMBINING ISOTOPIC AND GENETIC MARKERS TO IDENTIFY BREEDING ORIGINS OF MIGRANT BIRDS  

Microsoft Academic Search

A quantitative method for linking reproductive and nonreproductive phases of migratory life cycles is fundamental to understanding the biology of migratory organisms. Here we combine genetic (mtDNA) and biochemical (stable isotope) information to examine seasonal movements in the Swainson's Thrush ( Catharus ustulatus), a Neotropical migrant. We show that when these intrinsic markers are used in concert, they can predict

Jeffrey F. Kelly; Kristen C. Ruegg; Thomas B. Smith

2005-01-01

147

The use of genetic markers for parentage analysis in Passer domesticus (House Sparrows)  

Microsoft Academic Search

The relationships between 420 Passer domesticus (house sparrow) nestlings from 144 broods and the adults which fed them were determined using genetic markers. The inheritance and independence of six polymorphic enzymes observed with starch gel electrophoresis and the component bands of DNA fingerprint profiles were investigated, and the probabilities of detecting incorrect parental assignments calculated. Allozymes were capable of detecting

Jon H Wetton; David T Parkin; Royston E Carter

1992-01-01

148

DETERMINING GENETIC DIVERSITY AMONG LINES OF VIGNA UNGUICULATA SUBSPECIES BY AFLP AND SSR MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

AFLP and SSR markers were utilized to determine the genetic diversity among Vigna unguiculata subspecies. The three AFLP primer sets and the 10 SSR primer sets successfully identified very closely related accessions and a lack of homogeneity in some accessions. The AFLP methodology was successful f...

149

nature genetics volume 23 october 1999 203 Genome-wide mapping with biallelic markers  

E-print Network

the mapping of traits in diploid genomes. The cruciferous weed Arabidopsis thaliana is an attractive model. We developed a software package called InterMap and used it to automatically delimit Eds16 to a 7-cletter nature genetics · volume 23 · october 1999 203 Genome-wide mapping with biallelic markers

Howard, Martin

150

Random amplified polymorphic DNA (RAPD) markers for genetic analysis in micropropagated plants of Populus deltoides Marsh  

Microsoft Academic Search

RAPD markers were used to assess genetic fidelity of 23 micropropagated plants of a single clone (L34) of Populus deltoides. Eleven arbitrary 10-base primers were successfully used to amplify DNA from in vivo and in vitro material. Of these, 5 distinguished a total of 13 polymorphisms common across 6 micropropagated plants. Apart from these 6 plants, the amplification products were

Vijay Rani; Ajay Parida; S. N. Raina

1995-01-01

151

Study of genetic diversity in Chamomile ( Matricaria chamomilla) based on morphological traits and molecular markers  

Microsoft Academic Search

Chamomile is one of the most important medicinal plants in the world trade that has many applications in drug and sanitary industrials. In order to evaluate the genetic diversity of different chamomile landraces based on morphological and molecular markers, 20 landraces were collected from different area of Iran. In addition to that, five populations imported from European were examined. The

M. Solouki; H. Mehdikhani; H. Zeinali; A. A. Emamjomeh

2008-01-01

152

Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In...

153

Analysis of genetic diversity in Ganoderma population with a novel molecular marker SRAP  

Microsoft Academic Search

Genetic marker technology designed to detect naturally occurring polymorphisms at the DNA level had become an invaluable and revolutionizing tool for both applied and basic studies of fungi. To eliminate the confusion on the taxonomy of Ganoderma strains, in this study, a collection of 31 accessions representative of morphotypes and some unclassified types was used for analyzing molecular diversity using

Shu-Jing Sun; Wei Gao; Shu-Qian Lin; Jian Zhu; Bao-Gui Xie; Zhi-Bin Lin

2006-01-01

154

Genetic Diversity of Lablab (L. purpureus) Germplasm Assessed by SSR Markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

The genetic diversity of the USDA Lablab purpureus germplasm collection is unknown and was assessed by using polymorphic simple sequence repeat (SSR) markers derived from Medicago, soybean and cowpea. Phylogenetic analysis partitioned 47 representative accessions into two main clades (wild clade pr...

155

Genetic relationships among melon breeding lines revealed by RAPD markers and agronomic traits  

Microsoft Academic Search

RAPD} markers and agronomic traits were used to determine the genetic relationships among 32 breeding, lines of melon belonging to seven varietal types. Most of the breeding lines were Galia and Piel de Sapo genotypes, which are currently being used in breeding programmes to develop new hybrid combinations. A total of 115 polymorphic reliable bands from 43 primers and 24

E. Garcia; M. Jamilena; J. I. Alvarez; T. Arnedo; J. L. Oliver; R. Lozano

1998-01-01

156

The Use of Incompletely Linked Markers in Genetic Counseling: Accuracy versus Linkage  

Microsoft Academic Search

The utility of incompletely linked, selectively neutral, multiallelic markers for tracing the transmission of associated genes is examined theoretically for all genetic counseling situations in which the diagnosis of deleterious progeny is in question. The analysis focuses on the fraction of progeny from each two locus mating which can be diagnosed with minimal accuracy A solely on the basis of

Marjorie A. Asmussen

1985-01-01

157

Molecular genetic characterization of lasquerella new industrial crop using DArTseq markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

DArTseq, a new SNP-based marker platform, was developed and used to analyze the genetic diversity of the US germplasm collection of lesquerella. Lesquerella is a new oilseed crop in the Brassica family found native in the American Southwest. The potential of the species as a domestic source of indu...

158

Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genetic diversity of thirty five Psidium guajava accessions maintained at the USDA, National Plants Germplasm System, Hilo, HI, was characterized using 20 simple sequence repeat (SSR) markers. Diversity analysis detected a total of 178 alleles ranging from four to 16. The observed mean heterozygosit...

159

Assessment of genetic diversity in broomcorn millet ( Panicum miliaceum L.) using SSR markers  

Microsoft Academic Search

The genetic diversity of 118 accessions of broomcorn millet (Panicum miliaceum L.), collected from various ecological areas, wasanalyzed. Using 46 SSR (Simple Sequence Repeat) polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles werefound, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91.

Xingyu Hu; Jianfei Wang; Ping Lu; Hongsheng Zhang

2009-01-01

160

The use of genetic markers to estimate the frequency of successful alternative reproductive tactics  

Microsoft Academic Search

This paper outlines a method for estimating rates of successful alternative reproductive tactics from parental exclusions known through the use of genetic markers. We review a method for calculating the probability of excluding a putative father when he is not the actual father. We adapt this method to model two mating tactics of concern to sociobiologists: extrapair copulations (EPCs) and

David F. Westneat; Peter C. Frederick; R. Haven Wiley

1987-01-01

161

Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution? †  

PubMed Central

Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described bovine feces-specific genetic markers and a method for the enumeration of these markers using a Markov chain Monte Carlo approach. Both assays exhibited a range of quantification from 25 to 2 × 106 copies of target DNA, with a coefficient of variation of <2.1%. One of these assays can be multiplexed with an internal amplification control to simultaneously detect the bovine-specific genetic target and presence of amplification inhibitors. The assays detected only cattle fecal specimens when tested against 204 fecal DNA extracts from 16 different animal species and also demonstrated a broad distribution among individual bovine samples (98 to 100%) collected from five geographically distinct locations. The abundance of each bovine-specific genetic marker was measured in 48 individual samples and compared to quantitative PCR-enumerated quantities of rRNA gene sequences representing total Bacteroidetes, Bacteroides thetaiotaomicron, and enterococci in the same specimens. Acceptable assay performance combined with the prevalence of DNA targets across different cattle populations provides experimental evidence that these quantitative assays will be useful in monitoring bovine fecal pollution in ambient waters. PMID:18065617

Shanks, Orin C.; Atikovic, Emina; Blackwood, A. Denene; Lu, Jingrang; Noble, Rachel T.; Domingo, Jorge Santo; Seifring, Shawn; Sivaganesan, Mano; Haugland, Richard A.

2008-01-01

162

Common DNA Markers Can Account for More Than Half of the Genetic Influence on Cognitive Abilities  

PubMed Central

For nearly a century, twin and adoption studies have yielded substantial estimates of heritability for cognitive abilities, although it has proved difficult for genomewide-association studies to identify the genetic variants that account for this heritability (i.e., the missing-heritability problem). However, a new approach, genomewide complex-trait analysis (GCTA), forgoes the identification of individual variants to estimate the total heritability captured by common DNA markers on genotyping arrays. In the same sample of 3,154 pairs of 12-year-old twins, we directly compared twin-study heritability estimates for cognitive abilities (language, verbal, nonverbal, and general) with GCTA estimates captured by 1.7 million DNA markers. We found that DNA markers tagged by the array accounted for .66 of the estimated heritability, reaffirming that cognitive abilities are heritable. Larger sample sizes alone will be sufficient to identify many of the genetic variants that influence cognitive abilities. PMID:23501967

Haworth, Claire M. A.; Meaburn, Emma L.; Price, Thomas S.; Davis, Oliver S. P.

2013-01-01

163

Multi-marker-LD based genetic algorithm for tag SNP selection.  

PubMed

Despite the advances in genotyping technologies which have led to large reduction in genotyping cost, the Tag SNP Selection problem remains an important problem for computational biologists and geneticists. Selecting the smallest subset of tag SNPs that can predict the other SNPs would considerably minimize the complexity of genome-wide or block-based SNP-disease association studies. These studies would lead to better diagnosis and treatment of diseases. In this work, we propose three variations of a genetic algorithm based on two-marker linkage disequilibrium, multi-marker linkage disequilibrium, and a third measure that we denote by prediction power. The performance of the three algorithms are compared with those of a recognized tag SNP selection algorithm using three different real data sets from the HapMap project. The results indicate that the multi-marker linkage disequilibrium based genetic algorithm yields better prediction accuracy. PMID:25108458

Mouawad, Amer E; Mansour, Nashat

2014-12-01

164

A set of 37 microsatellite DNA markers for genetic diversity and structure analysis of Atlantic salmon Salmo salar populations.  

PubMed

Atlantic salmon Salmo salar microsatellite markers from a large database were analysed and selected with technical, economic and genetic criteria to provide an optimized set of polymorphic DNA markers for the analysis of the genetic diversity and the structure of anadromous Atlantic salmon populations. A set of 37 microsatellite markers was identified that are easy to use and provide a high level of differentiation power. PMID:20735571

Nikolic, N; Fève, K; Chevalet, C; Høyheim, B; Riquet, J

2009-02-01

165

A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis  

PubMed Central

Background Mitochondria (mt) contain their own autonomously replicating DNA, constituted as a small circular genome encoding essential subunits of the respiratory chain. Mt DNA is characterized by a genetic code which differs from the standard one. Interestingly, the mt genome of nematodes share some peculiar features, such as small transfer RNAs, truncated ribosomal RNAs and - in the class of Chromadorean nematodes - unidirectional transcription. Findings We present the complete mt genomic sequence (16,791 bp) of the plant-parasitic nematode Radopholus similis (class Chromadorea). Although it has a gene content similar to most other nematodes, many idiosyncrasies characterize the extremely AT-rich mt genome of R. similis (85.4% AT). The secondary structure of the large (16S) rRNA is further reduced, the gene order is unique, the large non-coding region contains two large repeats, and most interestingly, the UAA codon is reassigned from translation termination to tyrosine. In addition, 7 out of 12 protein-coding genes lack a canonical stop codon and analysis of transcriptional data showed the absence of polyadenylation. Northern blot analysis confirmed that only one strand is transcribed and processed. Furthermore, using nucleotide content bias methods, regions for the origin of replication are suggested. Conclusion The extraordinary mt genome of R. similis with its unique genetic code appears to contain exceptional features correlated to DNA decoding. Therefore the genome may provide an incentive to further elucidate these barely understood processes in nematodes. This comprehension may eventually lead to parasitic nematode-specific control targets as healthy mitochondria are imperative for organism survival. In addition, the presented genome is an interesting exceptional event in genetic code evolution. PMID:19778425

Jacob, Joachim EM; Vanholme, Bartel; Van Leeuwen, Thomas; Gheysen, Godelieve

2009-01-01

166

Maintaining genetic diversity using molecular coancestry: the effect of marker density and effective population size  

PubMed Central

Background The most efficient method to maintain genetic diversity in populations under conservation programmes is to optimize, for each potential parent, the number of offspring left to the next generation by minimizing the global coancestry. Coancestry is usually calculated from genealogical data but molecular markers can be used to replace genealogical coancestry with molecular coancestry. Recent studies showed that optimizing contributions based on coancestry calculated from a large number of SNP markers can maintain higher levels of diversity than optimizing contributions based on genealogical data. In this study, we investigated how SNP density and effective population size impact the use of molecular coancestry to maintain diversity. Results At low SNP densities, the genetic diversity maintained using genealogical coancestry for optimization was higher than that maintained using molecular coancestry. The performance of molecular coancestry improved with increasing marker density, and, for the scenarios evaluated, it was as efficient as genealogical coancestry if SNP density reached at least 3 times the effective population size. However, increasing SNP density resulted in reduced returns in terms of maintained diversity. While a benefit of 12% was achieved when marker density increased from 10 to 100 SNP/Morgan, the benefit was only 2% when it increased from 100 to 500 SNP/Morgan. Conclusions The marker density of most SNP chips already available for farm animals is sufficient for molecular coancestry to outperform genealogical coancestry in conservation programmes aimed at maintaining genetic diversity. For the purpose of effectively maintaining genetic diversity, a marker density of around 500 SNPs/Morgan can be considered as the most cost effective density when developing SNP chips for new species. Since the costs to develop SNP chips are decreasing, chips with 500 SNPs/Morgan should become available in a short-term horizon for non domestic species. PMID:24088414

2013-01-01

167

Enrichment of a papaya high-density genetic map with AFLP markers.  

PubMed

A high-density genetic linkage map of papaya, previously developed using an F2 mapping population derived from the intraspecific cross AU9 x SunUp, was enriched with AFLP markers. The comprehensive genetic map presented here spans 945.2 cM and covers 9 major and 5 minor linkage groups containing 712 SSR, 277 AFLP, and 1 morphological markers. The average marker density for the 9 major linkage groups is 0.9 cM between adjacent markers, and the total number of gaps >5 cM was reduced from 48 to 27 in the current map. AFLPs generated by EcoRI/MseI primer combinations were distributed throughout the 14 linkage groups and resulted in several large locus order rearrangements within the 9 major linkage groups. Integration of AFLP markers provided tighter linkage association between loci, leading to a reduction in map distance on LGs 1, 2, and 4, which were inflated in the previous map, and correction of the marker order on LG8. Suppression of recombination in the male-specific Y region (MSY) of LG1 is further validated by the addition of 27 sex co-segregating AFLP markers. A large region of distorted segregation surrounding the MSY spans 54.4 cM and represents approximately 71% of the linkage group. This comprehensive high-density genetic map provides a framework for mapping quantitative trait loci and for fine mapping as well as for comparative genomic studies of crop plant development and evolution. PMID:19767901

Blas, Andrea L; Yu, Qingyi; Chen, Cuixia; Veatch, Olivia; Moore, Paul H; Paull, Robert E; Ming, Ray

2009-08-01

168

Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa  

PubMed Central

Background Bituminaria bituminosa is a perennial legume species from the Canary Islands and Mediterranean region that has potential as a drought-tolerant pasture species and as a source of pharmaceutical compounds. Three botanical varieties have previously been identified in this species: albomarginata, bituminosa and crassiuscula. B. bituminosa can be considered a genomic 'orphan' species with very few genomic resources available. New DNA sequencing technologies provide an opportunity to develop high quality molecular markers for such orphan species. Results 432,306 mRNA molecules were sampled from a leaf transcriptome of a single B. bituminosa plant using Roche 454 pyrosequencing, resulting in an average read length of 345 bp (149.1 Mbp in total). Sequences were assembled into 3,838 isotigs/contigs representing putatively unique gene transcripts. Gene ontology descriptors were identified for 3,419 sequences. Raw sequence reads containing simple sequence repeat (SSR) motifs were identified, and 240 primer pairs flanking these motifs were designed. Of 87 primer pairs developed this way, 75 (86.2%) successfully amplified primarily single fragments by PCR. Fragment analysis using 20 primer pairs in 79 accessions of B. bituminosa detected 130 alleles at 21 SSR loci. Genetic diversity analyses confirmed that variation at these SSR loci accurately reflected known taxonomic relationships in original collections of B. bituminosa and provided additional evidence that a division of the botanical variety bituminosa into two according to geographical origin (Mediterranean region and Canary Islands) may be appropriate. Evidence of cross-pollination was also found between botanical varieties within a B. bituminosa breeding programme. Conclusions B. bituminosa can no longer be considered a genomic orphan species, having now a large (albeit incomplete) repertoire of expressed gene sequences that can serve as a resource for future genetic studies. This experimental approach was effective in developing codominant and polymorphic SSR markers for application in diverse genetic studies. These markers have already given new insight into genetic variation in B. bituminosa, providing evidence that a division of the botanical variety bituminosa may be appropriate. This approach is commended to those seeking to develop useful markers for genomic orphan species. PMID:22171578

2011-01-01

169

Incidence of the main genetic markers in glioblastoma multiforme is independent of tumor topology.  

PubMed

Glioblastoma multiforme (GBM) is the most common as well as the most aggressive type of primary brain tumor of astrocytic origin in adults. GBM is characterized by a high degree of intratumoral heterogeneity both in histomorphology and genetic changes. Trisomy/polysomy of chromosome 7, monosomy of chromosome 10, EGFR gene amplification and p53 deletion have been described as the typical genetic markers for tumor classification and prediction of possible response to therapy. Our work was based on detection of these four main genetic changes both in central and peripheral parts of the tumors to evaluate possible differences in the topological incidence of these genetic markers. Chromosomal abnormalities in tumor samples from a group of 21 patients surgically treated for GBM were characterized by means of the interphase-fluorescence in situ hybridization (I-FISH) technique using sets of centromere and locus-specific DNA probes. In addition, we performed a detailed analysis of one selected tumor sample using a genomic microarray system (GenoSensor Array 300) to characterize copy number changes of specific sequences and refine results obtained by I-FISH. However, the data show no significant differences in occurrence of the described genetic markers in either part of the tumor. PMID:17447852

Necesalová, E; Vranová, V; Kuglík, P; Cejpek, P; Jarosová, M; Pesáková, M; Relichová, J; Veselská, R

2007-01-01

170

An Integrated Genetic and Cytogenetic Map for Zhikong Scallop, Chlamys farreri, Based on Microsatellite Markers  

PubMed Central

The reliability of genome analysis and proficiency of genetic manipulation requires knowledge of the correspondence between the genetic and cytogenetic maps. In the present study, we integrated cytogenetic and microsatellite-based linkage maps for Zhikong scallop, Chlamys farreri. Thirty-eight marker-anchored BAC clones standing for the 19 linkage groups were used to be FISH probes. Of 38 BAC clones, 30 were successfully located on single chromosome by FISH and used to integrate the genetic and cytogenetic map. Among the 19 linkage groups, 12 linkage groups were physically anchored by 2 markers, 6 linkage groups were anchored by 1 marker, and one linkage group was not anchored any makers by FISH. In addition, using two-color FISH, six linkage groups were distinguished by different chromosomal location; linkage groups LG6 and LG16 were placed on chromosome 10, LG8 and LG18 on chromosome 14. As a result, 18 of 19 linkage groups were localized to 17 pairs of chromosomes of C. farreri. We first integrated genetic and cytogenetic map for C. farreri. These 30 chromosome specific BAC clones in the cytogenetic map could be used to identify chromosomes of C. farreri. The integrated map will greatly facilitate molecular genetic studies that will be helpful for breeding applications in C. farreri and the upcoming genome projects of this species. PMID:24705086

Fu, Xiaoteng; Liao, Huan; Li, Xuan; Zhan, Aibin; Zhang, Lingling; Wang, Shi; Huang, Xiaoting; Bao, Zhenmin

2014-01-01

171

Genetic Relationships of Ethnic Minorities in Southwest China Revealed by Microsatellite Markers  

PubMed Central

Population migrations in Southwest and South China have played an important role in the formation of East Asian populations and led to a high degree of cultural diversity among ethnic minorities living in these areas. To explore the genetic relationships of these ethnic minorities, we systematically surveyed the variation of 10 autosomal STR markers of 1,538 individuals from 30 populations of 25 ethnic minorities, of which the majority were chosen from Southwest China, especially Yunnan Province. With genotyped data of the markers, we constructed phylogenies of these populations with both DA and DC measures and performed a principal component analysis, as well as a clustering analysis by structure. Results showed that we successfully recovered the genetic structure of analyzed populations formed by historical migrations. Aggregation patterns of these populations accord well with their linguistic affiliations, suggesting that deciphering of genetic relationships does in fact offer clues for study of ethnic differentiation. PMID:20360948

Zhang, Feng; Huang, Xiaoqin; Lin, Keqin; Shi, Lei; Hu, Songnian; Chu, Jiayou; Wang, Duen-Mei

2010-01-01

172

Child height, health and human capital: Evidence using genetic markers  

PubMed Central

Height has long been recognized as being associated with better outcomes: the question is whether this association is causal. We use children's genetic variants as instrumental variables to deal with possible unobserved confounders and examine the effect of child/adolescent height on a wide range of outcomes: academic performance, IQ, self-esteem, depression symptoms and behavioral problems. OLS findings show that taller children have higher IQ, perform better in school, and are less likely to have behavioral problems. The IV results differ: taller girls (but not boys) have better cognitive performance and, in contrast to the OLS, greater height appears to increase behavioral problems.

von Hinke Kessler Scholder, Stephanie; Davey Smith, George; Lawlor, Debbie A.; Propper, Carol; Windmeijer, Frank

2013-01-01

173

First Haploid Genetic Map Based on Microsatellite Markers in Senegalese Sole (Solea senegalensis, Kaup 1858).  

PubMed

The Senegalese sole (Solea senegalensis, Kaup 1858) is a flatfish species of great value for aquaculture. In this study, we develop the first linkage map in this species based on microsatellite markers characterized from genomic DNA libraries and EST databases of Senegalese sole and from other flatfish species. Three reference gynogenetic families were obtained by chromosome-manipulation techniques: two haploid gynogenetics, used to assign and order microsatellites to linkage groups and another diploid gynogenetic family, used for estimating marker-centromere distances. The consensus map consists of 129 microsatellites distributed in 27 linkage groups (LG), with an average density of 4.7 markers per LG and comprising 1,004 centimorgans (cM). Additionally, 15 markers remained unlinked. Through half-tetrad analysis, we were able to estimate the centromere distance for 81 markers belonging to 24 LG, representing an average of 3 markers per LG. Comparative mapping was performed between flatfish species LG and model fish species chromosomes (stickleback, Tetraodon, medaka, fugu and zebrafish). The usefulness of microsatellite markers and the genetic map as tools for comparative mapping and evolution studies is discussed. PMID:25107689

Molina-Luzón, Ma Jesús; Hermida, Miguel; Navajas-Pérez, Rafael; Robles, Francisca; Navas, José Ignacio; Ruiz-Rejón, Carmelo; Bouza, Carmen; Martínez, Paulino; de la Herrán, Roberto

2015-02-01

174

Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers  

PubMed Central

Four Korean native cattle (KNC) breeds—Hanwoo, Chikso, Heugu, and Jeju black—are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources. PMID:25358313

Suh, Sangwon; Kim, Young-Sin; Cho, Chang-Yeon; Byun, Mi-Jeong; Choi, Seong-Bok; Ko, Yeoung-Gyu; Lee, Chang Woo; Jung, Kyoung-Sub; Bae, Kyoung Hun; Kim, Jae-Hwan

2014-01-01

175

Genetic markers and biomarkers for age-related macular degeneration  

PubMed Central

Age-related macular degeneration (AMD) is the leading cause of visual impairment and blindness in the USA. Although the treatment of AMD has evolved to include laser photocoagulation, photodynamic therapy, surgical macular translocation and antiangiogenesis agents, treatment options for advanced AMD are limited. Furthermore, the dry form of AMD, albeit less devastating than the wet form, has even fewer viable treatment options. This review summarizes the various biomarkers of AMD and analyzes whether or not they may one day be exploited to determine risks of disease onset, measure progression of disease or even assess the effects of treatment of AMD. Potential biomarkers are important to identify since some might be utilized to reflect the disease state of a particular patient and to individualize therapy. Although studies have yielded promising results for nutrient and inflammatory biomarkers, these results have been inconsistent. At present, the best available markers of AMD risk are single nucleotide polymorphisms (SNPs). SNPs in complement factor H (CFH) and PLEKHA1/ARMS2/HtrA1 capture a substantial fraction of AMD risk and permit the identification of individuals at high risk of developing AMD. PMID:17917691

Ross, Robert J; Verma, Varun; Rosenberg, Kevin I; Chan, Chi-Chao; Tuo, Jingsheng

2007-01-01

176

Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines.  

PubMed

BackgroundGenetic diversity provides the capacity for plants to meet changing environments. It is fundamentally important in crop improvement. Fifty-nine local maize lines developed at INERA and 41 exotic (temperate and tropical) inbred lines were characterized using 1057 SNP markers to (1) analyse the genetic diversity in a diverse set of maize inbred lines; (2) determine the level of genetic diversity in INERA inbred lines and patterns of relationships of these inbred lines developed from two sources; and (3) examine the genetic differences between local and exotic germplasms.ResultsRoger¿s genetic distance for about 64% of the pairs of lines fell between 0.300 and 0.400. Sixty one per cent of the pairs of lines also showed relative kinship values of zero. Model-based population structure analysis and principal component analysis revealed the presence of 5 groups that agree, to some extent, with the origin of the germplasm. There was genetic diversity among INERA inbred lines, which were genetically less closely related and showed a low level of heterozygosity. These lines could be divided into 3 major distinct groups and a mixed group consistent with the source population of the lines. Pairwise comparisons between local and exotic germplasms showed that the temperate and some IITA lines were differentiated from INERA lines. There appeared to be substantial levels of genetic variation between local and exotic germplasms as revealed by missing and unique alleles.ConclusionsAllelic frequency differences observed between the germplasms, together with unique alleles identified within each germplasm, shows the potential for a mutual improvement between the sets of germplasm. The results from this study will be useful to breeders in designing inbred-hybrid breeding programs, association mapping population studies and marker assisted breeding. PMID:25421948

Dao, Abdalla; Sanou, Jacob; Mitchell, Sharon E; Gracen, Vernon; Danquah, Eric Y

2014-11-25

177

Pollen genetic markers for detection of mutagens in the environment  

SciTech Connect

To utilize and exploit pollen for in situ mutagen monitoring, screening and toxicology, the range of genetic traits in pollen must be identified and analyzed. To be useful for the development of mutagen detection systems proteins should be: (1) activity stainable or immunologically identifiable in the pollen, (2) the products of one to three loci; and (3) gametophytic and nuclear in origin. Several proteins, including alcohol dehydrogenase in maize, which meet these criteria are discussed. The waxy locus in barley and maize which controls starch deposition for pollen screening and mutant detection. Thirty waxy mutant lines, induced by sodium azide and gamma-rays are characterized for spontaneous and induced reversion frequencies, allelism, karyotype, amylose content, and UDPglucose glucosyltransferase (waxy gene product) activity. Twelve mutant alleles are being mapped by recombinant frequencies.

Nilan, R.A.; Rosichan, J.L.; Arenaz, P.; Hodgdon, A.L.; Kleinhofs, A.

1980-01-01

178

Competitive Metagenomic DNA Hybridization Identifies Host-Specific Microbial Genetic Markers in Cow Fecal Samples†  

PubMed Central

Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host-specific markers. Here we describe the application of a genome fragment enrichment (GFE) method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, bovine fecal DNA was challenged against a porcine fecal DNA background to select for bovine-specific DNA sequences. Bioinformatic analyses of 380 bovine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode membrane-associated and secreted proteins. Oligonucleotide primers capable of annealing to select Bacteroidales-like bovine GFE sequences exhibited extremely high specificity (>99%) in PCR assays with total fecal DNAs from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different bovine sources. These data demonstrate that direct metagenomic DNA analysis by the competitive solution hybridization approach described is an efficient method for identifying potentially useful fecal genetic markers and for characterizing differences between environmental microbial communities. PMID:16751515

Shanks, Orin C.; Santo Domingo, Jorge W.; Lamendella, Regina; Kelty, Catherine A.; Graham, James E.

2006-01-01

179

Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow.  

PubMed

Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall-run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring-run offspring that returned in spring (spring run), and fall-run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11, and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing. PMID:24478800

O'Malley, Kathleen G; Jacobson, Dave P; Kurth, Ryon; Dill, Allen J; Banks, Michael A

2013-12-01

180

Small-scale field test of the genetically engineered lacZY marker  

SciTech Connect

Commercial genetic engineering is advancing into areas that require the small-scale introduction of genetically engineered microorganisms (GEMs) to better quantify variables that affect microorganism distribution and survival and to document potential long-term consequences. A recombinant DNA marker system, the lacZY marker, developed by the Monsanto Agricultural Co., enables the distribution and fate of marked fluorescent pseudomonad organisms to be monitored under actual field conditions. Critical evaluation of GEMs under field conditions is imperative if plant-beneficial effects are to be correlated with organism release. This paper evaluates the effectiveness of this marker system and its ability to facilitate the assessment of risks associated with deliberate environmental introductions of genetically engineered microorganisms. Results of prerelease contained growth chamber and field experiments demonstrated that: (1) the scientific risk assessment methodology adopted by Monsanto and approved by the U.S. Environmental Protection Agency was appropriate and comprehensive; (2) the deliberate introduction of a GEM did not pose unacceptable or unforeseen risks to human health or the environment; (3) the lacZY marker is an effective environmental tracking tool; and (4) regulatory oversight should reflect the expected risk and not be excessively burdensome for all GEMs.

Hattemer-Frey, H.A.; Brandt, E.J.; Travis, C.C. (Oak Ridge National Laboratory, TN (USA))

1990-06-01

181

Mapping and analysis of quantitative trait loci in Lycopersicon (tomato) with the aid of genetic markers using approximate maximum likelihood methods  

Microsoft Academic Search

1691 F-2 progeny of a cross between Lycopersicon esculentum and L pimpinellifolium grown under field conditions were scored for 18 quantitative traits of economic interest and 10 segregating genetic markers. Each parental strain was homozygous for one allele of each marker. Four of the markers were electrophoretic, and six were morphological. Three pairs of the genetic markers were linked. An

J I Weller

1987-01-01

182

Gene-Based Single Nucleotide Polymorphism Markers for Genetic and Association Mapping in Common Bean  

PubMed Central

Background In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. Results In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364?×?G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93?×?JALO EEP558 and DOR364?×?BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041?cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. Conclusions In short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop. PMID:22734675

2012-01-01

183

Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using Insertion-Deletion (InDel) and Simple Sequence Repeat (SSR) markers  

PubMed Central

Background Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design. Results Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines. Conclusions This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic drift or selection during breeding processes. Comparative analysis of allele distribution revealed genetic divergence between improved cultivars and landraces, as well as between cultivars released in different years. These results will be useful for assessing cultivars and for marker-assisted breeding in sesame. PMID:24641723

2014-01-01

184

Assessment of genetic diversity in broomcorn millet (Panicum miliaceum L.) using SSR markers.  

PubMed

The genetic diversity of 118 accessions of broomcorn millet (Panicum miliaceum L.), collected from various ecological areas, was analyzed. Using 46 SSR (Simple Sequence Repeat) polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles were found, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91. The range of polymorphism information content (PIC) was 0.284-0.980 (average, 0.793). The expected heterozygosity (He) varied from 0.346 to 0.989, with an average of 0.834. The average coefficient of the genetic similarity of SSR markers among the 118 accessions was 0.609, and it ranged from 0.461 to 0.851. The UPGMA (Unweight Pair Group Method with Arithmetic Mean) clustering analysis at the genetic similarity value of 0.609 grouped the 118 accessions into five groups. Mantel test meant that geographical origin and genetic distance presented positive correlation. The clustering results were consistent with known information on ecological growing areas. The genetic similarity coefficient of the accessions in the Loess Plateau ecotype was significantly lower than those in the other ecotypes. It indicates that the highest level of genetic diversity occurred in the Loess Plateau, which is probably the original site of Panicum miliaceum. PMID:19683672

Hu, Xingyu; Wang, Jianfei; Lu, Ping; Zhang, Hongsheng

2009-08-01

185

Linkage analysis of five new genetic markers of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae).  

PubMed

Five new autosomal recessive genes are described in the oriental fruit fly, Bactrocera dorsalis (Hendel). These genetic markers are associated into three linkage groups. The matte (mt) gene is linked to the previously described mandarin red (ma) gene, and the white puparium (wp) gene is linked to the white eye (we) and amethyst (am) loci. The third designated linkage group has the yellow eye (ye) marker. The we/we homozygote is epistatic to ye/ye, and each is epistatic to am/am and ma/ma. PMID:1624766

McCombs, S D; Saul, S H

1992-01-01

186

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers.  

PubMed

Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut. PMID:12502264

Massawe, F J; Dickinson, M; Roberts, J A; Azam-Ali, S N

2002-12-01

187

Analysis of genetic diversity in Larix gmelinii (Pinaceae) with RAPD and ISSR markers.  

PubMed

Dahurian larch (Larix gmelinii), a deciduous conifer, is the northernmost tree, native to eastern Siberia and nearby regions of China. We used growth traits and molecular markers to assess genetic variation in different L. gmelinii growing regions; 105 individual samples were collected from seven regions of the Qingshan Forestry Centre, Heilongjiang Province, China. The greatest genetic regional variation was seen in the Youhao area, based on coefficients of variation for tree height, diameter and volume (14.73, 28.25, and 55.27%, respectively). Analysis using molecular markers showed rich genetic diversity. The RAPD and ISSR methods both indicated that most variation came from within populations. The seven regions were divided into two groups (Daxing'an and Xiaoxing'an Mountain ranges) by RAPD cluster analysis: Tianchi, Xiaojiuya, Yuanjiang, and Taiping regions were placed in the first group at a genetic distance of 0.08; while the other regions were in the second group. The correlation between RAPD markers and geographical distance was significant, with a correlation coefficient of 0.752. PMID:23408406

Zhang, L; Zhang, H G; Li, X F

2013-01-01

188

Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers.  

PubMed

The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions of N. nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7 wild lotus. Our results showed that sacred lotus exhibited a low level of genetic diversity, which may attribute to asexual reproduction and long-term artificial selection. A dendrogram based on both AFLP and SSR clustering data showed that: (1) the seed lotus accessions and rhizome lotus accessions were distinctly clustered into different groups, which indicated the significant genetic differentiation between them. This may be attributed to the two modes of reproduction and lack of genetic exchange; (2) the accessions of Thailand wild lotus were separated from other wild lotus accessions. This implied that the Thailand lotus might be genetically differentiated from other wild lotuses. In addition, Mantel test conducted gave highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with the values of r = 0.941 and r = 0.879, respectively, indicating the higher efficiency of the combination of these techniques (AFLP and SSR) in estimation and validation of the genetic diversity among the accession of sacred lotus. This knowledge of the genetic diversity and genetic relatedness of N. nucifera is potentially useful to improve the current strategies in breeding and germplasm conservation to enhance the ornamental and economic value of sacred lotus. PMID:21735103

Hu, Jihong; Pan, Lei; Liu, Honggao; Wang, Shuzhen; Wu, Zhihua; Ke, Weidong; Ding, Yi

2012-04-01

189

Marker-Based Estimation of Genetic Parameters in Genomics  

PubMed Central

Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing ‘big’ genomic data sets. PMID:25025305

Hu, Zhiqiu; Yang, Rong-Cai

2014-01-01

190

The genetic structure of adders (Vipera berus) in Fennoscandia: congruence between different kinds of genetic markers.  

PubMed

In order to elucidate the colonization history of Fennoscandian adders (Vipera berus), the phylogeographical patterns of two nuclear sets of DNA markers (random amplified polymorphic DNA and microsatellite) are compared with that previously obtained from mitochondrial DNA. An eastern and a western lineage within Fennoscandian adders is readily distinguishable using both sets of nuclear markers, corroborating the hypothesis that the lineages stem from separate glacial refugia. Moreover, the same contact zones as were derived from mitochondrial data are clearly identifiable. Both sets of nuclear markers detect a high level of admixture across one zone in northern Finland, with introgression reaching far west into Sweden. PMID:15367127

Carlsson, M; Söderberg, L; Tegelström, H

2004-10-01

191

Genetic response from marker assisted selection in an outbred population for differing marker bracket sizes and with two identified quantitative trait loci.  

PubMed Central

Effect of flanking quantitative trait loci (QTL)-marker bracket size on genetic response to marker assisted selection in an outbred population was studied by simulation of a nucleus breeding scheme. In addition, genetic response with marker assisted selection (MAS) from two quantitative trait loci on the same and different chromosome(s) was investigated. QTL that explained either 5% or 10% of phenotypic variance were simulated. A polygenic component was simulated in addition to the quantitative trait loci. In total, 35% of the phenotypic variance was due to genetic factors. The trait was measured on females only. Having smaller marker brackets flanking the QTL increased the genetic response from MAS selection. This was due to the greater ability to trace the QTL transmission from one generation to the next with the smaller flanking QTL-marker bracket, which increased the accuracy of estimation of the QTL allelic effects. Greater negative covariance between effects at both QTL was observed when two QTL were located on the same chromosome compared to different chromosomes. Genetic response with MAS was greater when the QTL were on the same chromosome in the early generations and greater when they were on different chromosomes in the later generations of MAS. PMID:9539451

Spelman, R; Bovenhuis, H

1998-01-01

192

Unique apicomplexan IMC sub-compartment proteins are early markers for apical polarity in the malaria parasite  

PubMed Central

Summary The phylum Apicomplexa comprises over 5000 intracellular protozoan parasites, including Plasmodium and Toxoplasma, that are clinically important pathogens affecting humans and livestock. Malaria parasites belonging to the genus Plasmodium possess a pellicle comprised of a plasmalemma and inner membrane complex (IMC), which is implicated in parasite motility and invasion. Using live cell imaging and reverse genetics in the rodent malaria model P. berghei, we localise two unique IMC sub-compartment proteins (ISPs) and examine their role in defining apical polarity during zygote (ookinete) development. We show that these proteins localise to the anterior apical end of the parasite where IMC organisation is initiated, and are expressed at all developmental stages, especially those that are invasive. Both ISP proteins are N-myristoylated, phosphorylated and membrane-bound. Gene disruption studies suggest that ISP1 is likely essential for parasite development, whereas ISP3 is not. However, an absence of ISP3 alters the apical localisation of ISP1 in all invasive stages including ookinetes and sporozoites, suggesting a coordinated function for these proteins in the organisation of apical polarity in the parasite. PMID:24244852

Poulin, Benoit; Patzewitz, Eva-Maria; Brady, Declan; Silvie, Olivier; Wright, Megan H.; Ferguson, David J. P.; Wall, Richard J.; Whipple, Sarah; Guttery, David S.; Tate, Edward W.; Wickstead, Bill; Holder, Anthony A.; Tewari, Rita

2013-01-01

193

Genetic diversity and population differentiation in the cockle Cerastoderma edule estimated by microsatellite markers  

NASA Astrophysics Data System (ADS)

The edible cockle Cerastoderma edule is a marine bivalve commercially fished in several European countries that have lately suffered a significant decrease in production. Despite its commercial importance, genetic studies in this species are scarce. In this work, genetic diversity and population differentiation of C. edule has been assessed using 11 microsatellite markers in eight locations from the European Atlantic coast. All localities showed similar observed and expected heterozygosity values, but displayed differences in allelic richness, with lowest values obtained for localities situated farther north. Global Fst value revealed the existence of significant genetic structure; all but one locality from the Iberian Peninsula were genetically homogeneous, while more remote localities from France, The Netherlands, and Scotland were significantly different from all other localities. A combined effect of isolation by distance and the existence of barriers that limit gene flow may explain the differentiation observed.

Martínez, L.; Méndez, J.; Insua, A.; Arias-Pérez, A.; Freire, R.

2013-03-01

194

Genetic analysis of 430 Chinese Cynodon dactylon accessions using sequence-related amplified polymorphism markers.  

PubMed

Although Cynodon dactylon (C. dactylon) is widely distributed in China, information on its genetic diversity within the germplasm pool is limited. The objective of this study was to reveal the genetic variation and relationships of 430 C. dactylon accessions collected from 22 Chinese provinces using sequence-related amplified polymorphism (SRAP) markers. Fifteen primer pairs were used to amplify specific C. dactylon genomic sequences. A total of 481 SRAP fragments were generated, with fragment sizes ranging from 260-1800 base pairs (bp). Genetic similarity coefficients (GSC) among the 430 accessions averaged 0.72 and ranged from 0.53-0.96. Cluster analysis conducted by two methods, namely the unweighted pair-group method with arithmetic averages (UPGMA) and principle coordinate analysis (PCoA), separated the accessions into eight distinct groups. Our findings verify that Chinese C. dactylon germplasms have rich genetic diversity, which is an excellent basis for C. dactylon breeding for new cultivars. PMID:25338051

Huang, Chunqiong; Liu, Guodao; Bai, Changjun; Wang, Wenqiang

2014-01-01

195

Panmixia defines the genetic diversity of a unique arthropod-dispersed fungus specific to Protea flowers  

PubMed Central

Knoxdaviesia proteae, a fungus specific to the floral structures of the iconic Cape Floral Kingdom plant, Protea repens, is dispersed by mites phoretic on beetles that pollinate these flowers. Although the vectors of K. proteae have been identified, little is known regarding its patterns of distribution. Seed bearing infructescences of P. repens were sampled from current and previous flowering seasons, from which K. proteae individuals were isolated and cultured. The genotypes of K. proteae isolates were determined using 12 microsatellite markers specific to this species. Genetic diversity indices showed a high level of similarity between K. proteae isolates from the two different infructescence age classes. The heterozygosity of the population was high (0.74 ± 0.04), and exceptional genotypic diversity was encountered (? = 97.87%). Population differentiation was negligible, owing to the numerous migrants between the infructescence age classes (Nm = 47.83) and between P. repens trees (Nm = 2.96). Parsimony analysis revealed interconnected genotypes, indicative of recombination and homoplasies, and the index of linkage disequilibrium confirmed that outcrossing is prevalent in K. proteae ( = 0.0067; P = 0.132). The high diversity and panmixia in this population is likely a result of regular gene flow and an outcrossing reproductive strategy. The lack of genetic cohesion between individuals from a single P. repens tree suggests that K. proteae dispersal does not primarily occur over short distances via mites as hypothesized, but rather that long-distance dispersal by beetles plays an important part in the biology of these intriguing fungi. PMID:25535560

Aylward, Janneke; Dreyer, Léanne L; Steenkamp, Emma T; Wingfield, Michael J; Roets, Francois

2014-01-01

196

Using host-associated genetic markers to investigate sources of fecal contamination in two Vermont streams  

USGS Publications Warehouse

The use of host-associated Bacteroidales-based 16S ribosomal ribonucleic acid genetic markers was investigated as a tool for providing information to managers on sources of bacterial impairment in Vermont streams. The study was conducted during 2009 in two watersheds on the U.S. Environmental Protection Agency's 303(d) List of Impaired Waters, the Huntington and the Mettawee Rivers. Streamwater samples collected during high-flow and base-flow conditions were analyzed for concentrations of Escherichia coli (E. coli) and Bacteroidales genetic markers (General AllBac, Human qHF183 and BacHum, Ruminant BoBac, and Canid BacCan) to identify humans, ruminants, and canids as likely or unlikely major sources of fecal contamination. Fecal reference samples from each of the potential source groups, as well as from common species of wildlife, were collected during the same season and from the same watersheds as water samples. The results were combined with data from other states to assess marker cross reaction and to relate marker results to E. coli, the regulated water-quality parameter, with a higher degree of statistical significance. Results from samples from the Huntington River collected under different flow conditions on three dates indicated that humans were unlikely to be a major source of fecal contamination, except for a single positive result at one station that indicated the potential for human sources. Ruminants (deer, moose, cow, or sheep) were potential sources of fecal contamination at all six stations on the Huntington River during one high-flow event and at all but two stations during the other high-flow event. Canids were potential sources of fecal contamination at some stations during two high-flow events, with genetic-marker concentrations in samples from two of the six stations showing consistent positive results for canids for both storm dates. A base-flow sample showed no evidence of major fecal contamination in the Huntington River from humans, ruminants, or canids. Results from samples from the Mettawee River watershed collected during high-flow conditions (12 storm samples on 2 dates at 6 stations) indicated that there was no evidence of fecal contamination from humans in seven samples and possible evidence in five samples. Results for humans were positive for only one station during both storm events. For two of the five samples with evidence for human fecal contamination, results for two different human genetic markers agreed, but results from three samples were inconsistent. In samples from five of the six Mettawee stations, ruminants were a potential source of fecal contamination on at least one of the three sampled dates, including three positive results for the base-flow sample. Yet samples from all of the stations that showed positive results for ruminants did so for only one or two of the three sampled dates. Samples from only one of the six stations gave consistent results, which were negative for ruminants for all three dates. In the Mettawee River base-flow sample, humans were an unlikely source of major fecal contamination. Factors that may influence results and conclusions include the timing of sample collection relative to the storm event; variability of E. coli and Bacteroidales concentrations in fecal reference samples and in water; sampling and analytical errors; the potential cross reactivity of host-associated genetic markers; and different persistence and survival rates of E. coli bacteria and Bacteroidales genetic markers on land, in water, and by season. These factors interfere with the ability to directly relate Bacteroidales concentrations to E. coli concentrations in river samples. It must be recognized that while use of Bacteroidales genetic markers as a source tracking tool coupled with the interpretive approach described in this report cannot be used quantitatively to pinpoint sources, it can be used to exclude potential sources as major contributors to fecal contamination.

Medalie, Laura; Matthews, Leslie J.; Stelzer, Erin A.

2011-01-01

197

Genetic diversity analysis among collected purslane (Portulaca oleracea L.) accessions using ISSR markers.  

PubMed

Genetic diversity and relationships among 45 collected purslane accessions were evaluated using ISSR markers. The 28 primers gave a total of 167 bands, among which 163 were polymorphic (97.6%). The genetic diversity as estimated by Shannon's information index was 0.513, revealing a quite high level of genetic diversity in the germplasm. The average number of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC) and Nei's index were 5.96, 1.59, 0.43, 0.35 and 0.35, respectively. The UPGMA dendrogram based on Nei's genetic distance grouped the whole germplasm into 7 distinct clusters. The analysis of molecular variance (AMOVA) revealed that 89% of total variation occurred within population, while 11% were found among populations. Based on the constructed dendrogram using ISSR markers those accessions that are far from each other by virtue of genetic origin and diversity index (like Ac1 and Ac42; Ac19 and Ac45; Ac9 and Ac23; Ac18 and A25; Ac24 and Ac18) are strongly recommended to select as parent for future breeding program to develop high yielding and stress tolerant purslane variety in contribution to global food security. PMID:25468001

Alam, M Amirul; Juraimi, Abdul Shukor; Rafii, Mohd Yusop; Hamid, Azizah Abdul; Arolu, Ibrahim Wasiu; Abdul Latif, M

2015-01-01

198

A genome-wide association study to identify genetic markers associated with endometrial cancer grade  

E-print Network

MEETING ABSTRACT Open Access A genome-wide association study to identify genetic markers associated with endometrial cancer grade T O’Mara1,2, D Duffy2, DJ Thompson3, S Ahmed4, K Ferguson2, CS Healey4, ANECS2, G Montgomery2, M Shah4, J Morrison3, PP... of chemotherapeutic agents targeting aggressive disease. Genome-wide association studies (GWAS) have been successful in identifying common genetic variation involved in cancer susceptibility. Presently there are lim- ited published studies using GWAS data to identify...

2012-04-12

199

DNA polymorphisms amplified by arbitrary primers are useful as genetic markers.  

PubMed Central

Molecular genetic maps are commonly constructed by analyzing the segregation of restriction fragment length polymorphisms (RFLPs) among the progeny of a sexual cross. Here we describe a new DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence. These polymorphisms, simply detected as DNA segments which amplify from one parent but not the other, are inherited in a Mendelian fashion and can be used to construct genetic maps in a variety of species. We suggest that these polymorphisms be called RAPD markers, after Random Amplified Polymorphic DNA. Images PMID:1979162

Williams, J G; Kubelik, A R; Livak, K J; Rafalski, J A; Tingey, S V

1990-01-01

200

A genetic linkage map of Silene vulgaris based on AFLP markers.  

PubMed

A genetic linkage map of an intraspecific cross between 2 Silene vulgaris s.l. ecotypes is presented. Three-hundred AFLP markers from 2 different restriction enzyme combinations were used to genotype an F2 mapping population. Maternal and paternal pure-coupling phase maps with 114 and 186 markers on 12 and 13 linkage groups, respectively, were constructed. Total map length of the paternal and maternal maps are 547 and 446 Kosambi cM, respectively. Nearly half of the markers (49%) exhibited significant transmission ratio distortion. Genome coverage and potential causes of the observed segregation ratio distortions are discussed. The maps represent a first step towards the identification of quantitative trait loci associated with habitat adaptation in the non-model species Silene vulgaris. PMID:16699551

Bratteler, Martin; Lexer, Christian; Widmer, Alex

2006-04-01

201

Genetic linkage map of human chromosome 7 with 63 DNA markers.  

PubMed Central

High-density genetic maps of individual human chromosomes will permit accurate localization of disease-associated genes and provide signposts that will be useful in the construction of physical maps. We have constructed a genetic map of chromosome 7 with 63 polymorphic DNA markers by using segregation data from 23 three-generation families and recently developed multilocus linkage-analysis techniques. The map spans 250 centimorgans in females and 170 centimorgans in males, with much of the difference being concentrated in a few intervals. The density and informativeness of the markers are such that there is a high probability of detecting linkage to any disease gene on this chromosome for which 20 phase-known meioses are available. Images PMID:2891136

Barker, D; Green, P; Knowlton, R; Schumm, J; Lander, E; Oliphant, A; Willard, H; Akots, G; Brown, V; Gravius, T

1987-01-01

202

The Drosophila melanogaster cinnabar gene is a cell autonomous genetic marker in Aedes aegypti (Diptera: Culicidae).  

PubMed

The cinnabar gene of Drosophila melanogaster (Meigen) encodes for kynurenine hydroxylase, an enzyme involved in ommochrome biosynthesis. This gene is commonly included as a visible genetic marker in gene vectors used to create transgenic Aedes aegypti (L.) that are homozygous for the khw allele, the mosquito homolog of cinnabar. Unexpectedly, the phenotype of cells expressing kynurenine hydroxylase in transgenic Ae. aegypti is cell autonomous as demonstrated by the recovery of insects heterozygous for the kynurenine hydroxylase transgene with mosaic eye color patterns. In addition, a transgenic gynandromorph was recovered in which one-half of the insect was expressing the kynurenine hydroxylase transgene, including one eye with red pigmentation, whereas the other half of the insect was homozygous khw and included a white eye. The cell autonomous behavior of cinnabar in transgenic Ae. aegypti is unexpected and increases the utility of this genetic marker. PMID:16119567

Sethuraman, Nagaraja; O'Brochta, David A

2005-07-01

203

A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development.  

PubMed

Tobacco (Nicotiana tabacum L.) is a species in the large family of the Solanaceae and is important as an agronomic crop and as a model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available that can be used for genome analysis, genetic mapping and breeding. We report here on the development and characterization of 5,119 new and functional microsatellite markers and on the generation of a high-resolution genetic map for the tetraploid tobacco genome. The genetic map was generated using an F2 mapping population derived from the intervarietal cross of Hicks Broadleaf × Red Russian and merges the polymorphic markers from this new set with those from a smaller set previously used to produce a lower density map. The genetic map described here contains 2,317 microsatellite markers and 2,363 loci, resulting in an average distance between mapped microsatellite markers which is less than 2 million base pairs or 1.5 cM. With this new and expanded marker resource, a sufficient number of markers are now available for multiple applications ranging from tobacco breeding to comparative genome analysis. The genetic map of tobacco is now comparable in marker density and resolution with the best characterized genomes of the Solanaceae: tomato and potato. PMID:21461649

Bindler, Gregor; Plieske, Jörg; Bakaher, Nicolas; Gunduz, Irfan; Ivanov, Nikolai; Van der Hoeven, Rutger; Ganal, Martin; Donini, Paolo

2011-07-01

204

Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers.  

PubMed

Persian oak (Quercus brantii Lindl.) is one of the most important woody species of the Zagros forests in Iran. Three molecular marker techniques: start codon targeted (SCoT), inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) markers were compared for fingerprinting of 125 individuals of this species collected from different geographical locations of north-west of Iran. A total of 233 bands were amplified by 18 ISSR primers, of which 224 (96.10%) were polymorphic, and 126 polymorphic bands (97.65%) were observed in 129 bands amplified by 10 IRAP primers. Besides, 118 bands were observed for all 10 SCoT primers, of which 113 were polymorphic (95.71%). Average polymorphism information content (PIC) for ISSR, IRAP and SCoT markers was 0.30, 0.32 and 0.38, respectively, and this revealed that SCoT markers were more informative than IRAP and ISSR for the assessment of diversity among individuals. Based on the three different molecular types, cluster analysis revealed that 125 individuals taken for the analysis can be divided into three distinct clusters. The Jaccard's genetic similarity based on the combined data ranged from 0.23 to 0.76. These results suggest that efficiency of SCoT, IRAP and ISSR markers was relatively the same in fingerprinting of individuals. All molecular marker types revealed a low genetic differentiation among populations, indicating the possibility of gene flow between the studied populations. These results have an important implication for Persian oak (Q. brantii) germplasm characterization, improvement, and conservation. PMID:25241382

Alikhani, Leila; Rahmani, Mohammad-Shafie; Shabanian, Naghi; Badakhshan, Hedieh; Khadivi-Khub, Abdollah

2014-11-15

205

Genetic analysis of apomixis in Citrus and Poncirus by molecular markers  

Microsoft Academic Search

Propagation of citrus rootstocks depends upon the production of clonal plants from nucellar seedlings. This makes apomixis\\u000a one of the host important traits in breeding programs for citrus rootstocks. The genetic control of apomixis was studied in\\u000a a 50-tree progeny derived from the cross C. volkameriana?P. trifoliata using 69 molecular markers and bulked segregant analysis. The proportion of nucellar seedlings

R. García; M. J. Asíns; J. Forner; E. A. Carbonell

1999-01-01

206

Assessment of genetic fidelity of micropropagated Swertia chirayita plantlets by ISSR marker assay  

Microsoft Academic Search

Inter simple sequence repeat (ISSR) marker assay was employed to validate the genetic fidelity of Swertia chirayita plantlets multiplied in vitro by axillary multiplication upto forty-two passages. Sixteen ISSR primers generated a total of 102 amplicons among the tissue-cultured\\u000a plants. Forty-eight amplicons were amplified in the outlier (a Swertia species). The outlier (negative control) was employed to rule out the

P. Joshi; V. Dhawan

2007-01-01

207

Analysis of genetic diversity in Agave tequilana var. Azul using RAPD markers  

Microsoft Academic Search

By federal law in Mexico, A. tequilana Weber var. Azul is the only variety of agave permitted for the production of any tequila. Our objective was to assay levels\\u000a of genetic variation in field populations of A. tequilana var. Azul using randomly amplified polymorphic DNA (RAPD) markers. Ten plants were collected from each of four different\\u000a fields, with two fields

Katia Gil Vega; Mario González Chavira; Octavio Martínez de la Vega; June Simpson; George Vandemark

2001-01-01

208

UNC study finds genetic marker in vitamin D receptor gene associated with increased pancreatic cancer survival  

Cancer.gov

Pancreatic cancer patients with a genetic marker linked to increased expression of the receptor for vitamin D have higher rates of overall survival, according to findings presented at the American Association for Cancer Research's Pancreatic Cancer: Progress and Challenges conference, held in Lake Tahoe, Nev., June 18-21. The study was conducted by scientists from the University of North Carolina at Chapel Hill Eshelman School of Pharmacy. UNC is home to the Lineberger Comprehensive Cancer Center.

209

Genetic relationships in the peregrine falcon (Falco peregrinus) analysed by microsatellite DNA markers.  

PubMed

Microsatellite DNA markers were developed from a peregrine falcon (Falco peregrinus) and genetic relationships among peregrine falcons in southern Norway were analysed using the markers. The genomic DNA library was screened for the presence of dinucleotide microsatellite repeats. Twelve loci revealed polymorphism through the initial analysis of 24 unrelated peregrine falcons, and Mendelian inheritance was confirmed in two peregrine falcon families bred in captivity. The estimated mean probability of identical genotypes in two unrelated individuals was 3 x 10-8, and the combined exclusion probability for parentage testing was 0.99 and 0.94 for one or both parents unknown, respectively. The markers were used to investigate the parentage of peregrine broods from the same nest site from different breeding seasons, and subsequently the nest-site fidelity of the breeding peregrines. High nest-site fidelity was found by studying pairwise comparisons of relatedness (rxy) estimates among chicks at six nest sites from three different breeding seasons. Cross-species amplifications showed that most loci also appeared to amplify polymorphic products in the gyrfalcon (F. rusticolus), merlin (F. columbarius), hobby (F. subbuteo) and kestrel (F. tinnunculus), demonstrating that the loci will provide powerful genetic markers in these falcons too. PMID:10652075

Nesje, M; Røed, K H; Lifjeld, J T; Lindberg, P; Steen, O F

2000-01-01

210

Brucellosis outbreak in a Swedish kennel in 2013: Determination of genetic markers for source tracing.  

PubMed

Brucellosis is a highly infectious zoonotic disease but rare in Sweden. Nonetheless, an outbreak of canine brucellosis caused by an infected dog imported to Sweden was verified in 2013. In total 25 dogs were tested at least duplicated by the following approaches: real-time PCR for the detection of Brucella canis, a Brucella genus-specific real-time PCR, selective cultivation, and microscopic examination. The whole genome of B. canis strain SVA13 was analysed regarding genetic markers for epidemiological examination. The genome of an intact prophage of Roseobacter was detected in B. canis strain SVA13 with whole genome sequence prophage analysis (WGS-PA). It was shown that the prophage gene content in the American, African and European isolates differs remarkably from the Asian strains. The prophage sequences in Brucella may therefore serve of use as genetic markers in epidemiological investigations. Phage DNA fragments were also detected in clustered, regularly interspaced short palindromic repeats (CRISPR) in the genome of strain SVA13. In addition to the recommendations for genetic markers in Brucella outbreak tracing, our paper reports a validated two-step stand-alone real-time PCR for the detection of B. canis and its first successful use in an outbreak investigation. PMID:25465667

Kaden, Rene; Ågren, Joakim; Båverud, Viveca; Hallgren, Gunilla; Ferrari, Sevinc; Börjesson, Joann; Lindberg, Martina; Bäckman, Stina; Wahab, Tara

2014-12-01

211

Immunohistochemical expression of myoepithelial markers in adenomyoepithelioma of the breast: a unique paradoxical staining pattern of high-molecular weight cytokeratins.  

PubMed

To determine which immunohistochemical markers are useful for the identification of neoplastic myoepithelial cells in adenomyoepithelioma of the breast, the expression of seven myoepithelial markers (?-smooth muscle actin (?-SMA), calponin, p63, CD10, cytokeratin 5/6, cytokeratin 14, and S-100) was examined in 19 lesions from 16 patients. The lesion consisted of seven spindle and 12 clear cell lesions. For normal myoepithelial cells, ?-SMA, calponin, and p63 were significantly more sensitive than cytokeratin 5/6, cytokeratin 14, and S-100. There was no significant difference in the expression of ?-SMA, calponin, p63, and CD10 in neoplastic myoepithelial cells of adenomyoepithelioma regardless of spindle or clear cell types. In spindle cell lesions, high-molecular weight cytokeratins (HMWCK; cytokeratin 5/6 and cytokeratin 14) tended to show higher staining scores and S-100 showed lower staining scores than other markers. In clear cell lesions, HMWCK showed significantly lower staining scores than the other five markers. There was no significant difference in staining scores among the other five markers. HMWCK showed a unique paradoxical staining pattern in clear cell lesions, with diffusely positive inner epithelial cells and completely negative outer myoepithelial cells. Although the sensitivity of HMWCK in clear cell lesions is low, with this unique paradoxical staining pattern and relatively high sensitivity in spindle cell lesions, HMWCK could be useful in diagnosing adenomyoepithelioma. In choosing immunohistochemical markers, any of the seven markers are useful, but combining HMWCK and any one of ?-SMA, calponin, and p63 would be a good panel for the diagnosis of adenomyoepithelioma. PMID:25479938

Moritani, Suzuko; Ichihara, Shu; Yatabe, Yasushi; Hasegawa, Masaki; Iwakoshi, Akari; Hosoda, Waki; Narita, Michihiko; Nagai, Yuichiro; Asai, Masami; Ujihira, Nobuko; Yuba, Yoshiaki; Jijiwa, Mayumi

2014-12-01

212

Multi-Genetic Marker Approach and Spatio-Temporal Analysis Suggest There Is a Single Panmictic Population of Swordfish Xiphias gladius in the Indian Ocean  

PubMed Central

Genetic population structure of swordfish Xiphias gladius was examined based on 2231 individual samples, collected mainly between 2009 and 2010, among three major sampling areas within the Indian Ocean (IO; twelve distinct sites), Atlantic (two sites) and Pacific (one site) Oceans using analysis of nineteen microsatellite loci (n?=?2146) and mitochondrial ND2 sequences (n?=?2001) data. Sample collection was stratified in time and space in order to investigate the stability of the genetic structure observed with a special focus on the South West Indian Ocean. Significant AMOVA variance was observed for both markers indicating genetic population subdivision was present between oceans. Overall value of F-statistics for ND2 sequences confirmed that Atlantic and Indian Oceans swordfish represent two distinct genetic stocks. Indo-Pacific differentiation was also significant but lower than that observed between Atlantic and Indian Oceans. However, microsatellite F-statistics failed to reveal structure even at the inter-oceanic scale, indicating that resolving power of our microsatellite loci was insufficient for detecting population subdivision. At the scale of the Indian Ocean, results obtained from both markers are consistent with swordfish belonging to a single unique panmictic population. Analyses partitioned by sampling area, season, or sex also failed to identify any clear structure within this ocean. Such large spatial and temporal homogeneity of genetic structure, observed for such a large highly mobile pelagic species, suggests as satisfactory to consider swordfish as a single panmictic population in the Indian Ocean. PMID:23717447

Muths, Delphine; Le Couls, Sarah; Evano, Hugues; Grewe, Peter; Bourjea, Jerome

2013-01-01

213

Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers  

NASA Astrophysics Data System (ADS)

Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

2014-08-01

214

Genetic Relationships of Aglaonema Species and Cultivars Inferred from AFLP Markers  

PubMed Central

• Background and Aims Aglaonema is an important ornamental foliage plant genus, but genetic relationships among its species and cultivars have not been reported. This study analysed genetic relatedness of 54 cultivars derived from nine species using amplified fragment length polymorphism (AFLP) markers. • Methods Initially, 48 EcoRI + 2/MseI + 3 primer set combinations were screened, from which six primer sets that showed clear scoreable and highly polymorphic fragments were selected and used for AFLP reactions. AFLP fragments were scored and entered into a binary data matrix as discrete variables. Jaccard’s coefficient of similarity was calculated for all pair?wise comparisons among the 54 cultivars, and a dendrogram was constructed by the unweighted pair?group method using the arithmetic average (UPGMA). • Key Results The number of AFLP fragments generated per primer set ranged from 59 to 112 with fragment sizes varying from 50 to 565 bp. A total of 449 AFLP fragments was detected, of which 314 were polymorphic (70 %). All cultivars were clearly differentiated by their AFLP fingerprints. The 54 cultivars were divided into seven clusters; cultivars within each cluster generally share similar morphological characteristics. Cluster I contains 35 cultivars, most of them are interspecific hybrids developed mainly from A. commutatum, A. crispum or A. nitidum. However, Jaccard’s similarity coefficients among these hybrids are 0·84 or higher, suggesting that these popular hybrid cultivars are genetically much closer than previously thought. This genetic similarity may imply that A. nitidum and A. crispum are likely progenitors of A. commutatum. • Conclusions Results of this study demonstrate the efficiency and ease of using AFLP markers for investigating genetic relationships of ornamental foliage plants, a group usually propagated vegetatively. The AFLP markers developed will help future Aglaonema cultivar identification, germplasm conservation and new cultivar development. PMID:14726418

CHEN, JIANJUN; DEVANAND, PACHANOOR S.; NORMAN, DAVID J.; HENNY, RICHARD J.; CHAO, CHIH?CHENG T.

2004-01-01

215

Random amplified polymorphic markers as indicator for genetic conservation program in Iranian pheasant (Phasianus colchicus).  

PubMed

The objective of present study was identification of genetic similarity between wild Iran and captive Azerbaijan Pheasant using PCR-RAPD markers. For this purpose, in overall, 28 birds were taken for DNA extraction and subsequently 15 arbitrary primers were applied for PCR-RAPD technique. After electrophoresis, five primers exhibited sufficient variability which yielded overall 65 distinct bands, 59 polymorphic bands, for detalis, range of number of bands per primer was 10 to 14, and produced size varied between 200 to 1500?bp. Highest and lowest polymorphic primers were OPC5, OPC16 (100%) and OPC15 (81%), respectively. Result of genetic variation between two groups was accounted as nonsignificant (8.12%) of the overall variation. According to our expectation the wild Iranian birds showed higher genetic diversity value than the Azerbaijan captive birds. As general conclusion, two pheasant populations have almost same genetic origin and probably are subpopulations of one population. The data reported herein could open the opportunity to search for suitable conservation strategy to improve richness of Iran biodiversity and present study here was the first report that might have significant impact on the breeding and conservation program of Iranian pheasant gene pool. Analyses using more regions, more birds, and more DNA markers will be useful to confirm or to reject these findings. PMID:23002388

Elyasi Zarringhabaie, Ghorban; Javanmard, Arash; Pirahary, Ommolbanin

2012-01-01

216

Random Amplified Polymorphic Markers as Indicator for Genetic Conservation Program in Iranian Pheasant (Phasianus colchicus)  

PubMed Central

The objective of present study was identification of genetic similarity between wild Iran and captive Azerbaijan Pheasant using PCR-RAPD markers. For this purpose, in overall, 28 birds were taken for DNA extraction and subsequently 15 arbitrary primers were applied for PCR-RAPD technique. After electrophoresis, five primers exhibited sufficient variability which yielded overall 65 distinct bands, 59 polymorphic bands, for detalis, range of number of bands per primer was 10 to 14, and produced size varied between 200 to 1500?bp. Highest and lowest polymorphic primers were OPC5, OPC16 (100%) and OPC15 (81%), respectively. Result of genetic variation between two groups was accounted as nonsignificant (8.12%) of the overall variation. According to our expectation the wild Iranian birds showed higher genetic diversity value than the Azerbaijan captive birds. As general conclusion, two pheasant populations have almost same genetic origin and probably are subpopulations of one population. The data reported herein could open the opportunity to search for suitable conservation strategy to improve richness of Iran biodiversity and present study here was the first report that might have significant impact on the breeding and conservation program of Iranian pheasant gene pool. Analyses using more regions, more birds, and more DNA markers will be useful to confirm or to reject these findings. PMID:23002388

Elyasi Zarringhabaie, Ghorban; Javanmard, Arash; Pirahary, Ommolbanin

2012-01-01

217

A genetic map of melon ( Cucumis melo L.) with RFLP, RAPD, isozyme, disease resistance and morphological markers  

Microsoft Academic Search

One hundred and ten markers were analysed for linkage in 218 F2 plants derived from two divergent cultivars (Védrantais and Songwhan Charmi) of Cucumis melo (L.). Thirty-four RFLPs, 64 RAPDs, one isozyme, four disease resistance markers and one morphological marker were used to construct a genetic map spanning 14 linkage groups covering 1390 cM of the melon genome. RAPD and

S. Baudracco-Arnas; M. Pitrat

1996-01-01

218

Comparison of genetic and cytogenetic maps of hexaploid wheat ( Triticum aestivum L.) using SSR and DArT markers  

Microsoft Academic Search

A number of technologies are available to increase the abundance of DNA markers and contribute to developing high resolution\\u000a genetic maps suitable for genetic analysis. The aim of this study was to expand the number of Diversity Array Technology (DArT)\\u000a markers on the wheat array that can be mapped in the wheat genome, and to determine their chromosomal location with

Michael G. Francki; Esther Walker; Allison C. Crawford; Sue Broughton; Herbert W. Ohm; Iain Barclay; Robin E. Wilson; Robyn McLean

2009-01-01

219

Potential Vulnerability Markers within the Affective Domain in Subjects at Genetic and Clinical High Risk for Schizophrenia  

Microsoft Academic Search

Background: Relative to ample high-risk studies on neurocognitive function, only a few high-risk studies have examined affective functioning components as possible vulnerability markers. In this study, we comprehensively assessed baseline affective functioning in subjects at clinical high risk (CHR) and genetic high risk (GHR) for schizophrenia, and healthy controls (HC), and compared the results to elucidate possible vulnerability markers in

Seung Jae Lee; So Young Yoo; Do-Hyung Kang; Kyung Jin Lee; Tae Hyun Ha; Whee Wee; Ae-Ra Lee; Nam Sick Kim; Jun Soo Kwon

2008-01-01

220

Analysis of a Detailed Genetic Linkage Map of Lactuca sativa (Lettuce) Constructed From RFLP and RAPD Markers  

Microsoft Academic Search

A detailed genetic map has been constructed from the F, population of a single intraspecific cross of Lactuca sativa (n = 9). It comprises 319 loci, including 152 restriction fragment length polymorphism (RFLP), 130 random amplified polymorphic DNA (RAPD), 7 isozyme, 19 disease resistance, and 11 morphological markers. Thirteen major, four minor linkage groups and several unlinked markers are identified

Rick V. Kesseli; Pt Ilan Parant; Richard W. Michelmore

221

Comparison between RAPD and SSR molecular markers in detecting genetic variation in kiwifruit ( Actinidia deliciosa A. Chev)  

Microsoft Academic Search

Two different DNA-based techniques, random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers, were used for fingerprinting kiwifruit genotypes and for detecting undesirable genetic variation in micropropagated plants. The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Two cluster analyses

M. A. Palombi; C. Damiano

2002-01-01

222

Questionable Specificity of Genetic Total Faecal Pollution Markers for Integrated Water Quality Monitoring and Source Tracking  

NASA Astrophysics Data System (ADS)

Characterisation of microbial faecal hazards in water is a fundamental aspect for target-orientated water resources management to achieve appropriate water quality for various purposes like water supply or agriculture and thus to minimize related health risks. Nowadays the management of water resources increasingly demands detailed knowledge on the extent and the origin of microbial pollution. Cultivation of standard faecal indicator bacteria, which has been used for over a century to test the microbiological water quality, cannot sufficiently meet these challenges. The abundant intestinal bacterial populations are very promising alternative targets for modern faecal indication systems. Numerous assays for the detection of genetic markers targeting source-specific populations of the phylum Bacteroidetes have been developed in recent years. In some cases markers for total faecal pollution were also proposed in order to relate source-specific marker concentrations to general faecal pollution levels. However, microbial populations in intestinal and non-intestinal systems exhibit a dazzling array of diversity and molecular analysis of microbial faecal pollution has been based on a fragmentary puzzle of very limited sequence information. The aim of this study was to test the available qPCR-based methods detecting genetic Bacteroidetes markers for total faecal pollution in terms of their value and specificity as indicators of faecal pollution. We applied the AllBac (Layton et al., 2006) the BacUni (Kildare et al., 2007) and the Bacteroidetes (Dick and Field, 2004) assays on soil DNA samples. Samples were collected in well characterised karst spring catchments in Austria's Eastern Calcareous Alps. They were at various levels of altitude between 800 and 1800 meters above sea level and from several different habitats (woodland, alpine pastures, krummholz). In addition we tried to choose sampling sites representing a presumptive gradient of faecal pollution levels. For example sites with obvious faecal influence (e.g. right next to a cowpat) were included as well as more pristine sites without faecal influence from large animals (e.g. fenced areas). Surprisingly, results from investigations with the AllBac assay showed concentrations of the total faecal marker in soil in the range of 106 to 109 Marker Equivalents per g of soil, which is equal or only slightly lower than the concentrations of this particular marker in faeces or raw sewage. Preliminary results from the other tested assays seem to confirm that the targeted markers are also highly abundant in soils. In addition, the markers were present in comparable concentrations in soils from pristine locations as well as in soils under the potential influence of faeces giving a strong indication that these methods also target non-intestinal, autochthonous soil populations. In contrast, source-specific markers (ruminant-specific BacR and human-specific BacH, Reischer et al., 2007, 2006) could only be detected in 30 to 50% of the soil samples at concentrations close to the detection limit, which is at least four orders of magnitude lower than in faecal samples of the respective target sources, ruminant animals and humans. The achieved results call the applicability of the proposed qPCR-based assays for total faecal pollution into question. In fact the assays do not seem to be specific for intestinal Bacteroidetes populations at all and the respective marker concentration levels in pristine soils negate their applicability in the investigated areas. This study also emphasizes the need to test the specificity and sensitivity of qPCR-based assays for total faecal pollution on the local level and especially against non-intestinal environmental samples, which might contribute to marker levels in the aquatic compartment. In conclusion there is a strong demand for marker-based detection techniques for total faecal pollution in water quality monitoring and risk assessment but currently none of the tested assays seems to meet the methodical requirements.

Vierheilig, Julia; Reischer, Georg H.; Farnleitner, Andreas H.

2010-05-01

223

Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform  

PubMed Central

Next-generation sequencing is a fast and cost-effective way to obtain sequence data for nonmodel organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptome data of a single Triturus species and design 96 primer pairs that amplify c. 180 bp fragments positioned in 3-prime untranslated regions. Next, these markers are tested with uniplex PCR for a set of species spanning the taxonomical width of the genus Triturus. The 52 markers that consistently show a single band of expected length at gel electrophoreses for all tested crested newt species are then amplified in five multiplex PCRs (with a plexity of ten or eleven) for 132 individual newts: a set of 84 representing the seven (candidate) species and a set of 48 from a presumed hybrid population. After pooling multiplexes per individual, unique tags are ligated to link amplicons to individuals. Subsequently, individuals are pooled equimolar and sequenced on the Ion Torrent next-generation sequencing platform. A bioinformatics pipeline identifies the alleles and recodes these to a genotypic format. Next, we test the utility of our markers. baps allocates the 84 crested newt individuals representing (candidate) species to their expected (candidate) species, confirming the markers are suitable for species delineation. newhybrids, a hybrid index and hiest confirm the 48 individuals from the presumed hybrid population to be genetically admixed, illustrating the potential of the markers to identify interspecific hybridization. We expect the set of markers we designed to provide a high resolving power for analysis of hybridization in Triturus. PMID:24571307

Wielstra, B; Duijm, E; Lagler, P; Lammers, Y; Meilink, W R M; Ziermann, J M; Arntzen, J W

2014-01-01

224

Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform.  

PubMed

Next-generation sequencing is a fast and cost-effective way to obtain sequence data for nonmodel organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptome data of a single Triturus species and design 96 primer pairs that amplify c. 180 bp fragments positioned in 3-prime untranslated regions. Next, these markers are tested with uniplex PCR for a set of species spanning the taxonomical width of the genus Triturus. The 52 markers that consistently show a single band of expected length at gel electrophoreses for all tested crested newt species are then amplified in five multiplex PCRs (with a plexity of ten or eleven) for 132 individual newts: a set of 84 representing the seven (candidate) species and a set of 48 from a presumed hybrid population. After pooling multiplexes per individual, unique tags are ligated to link amplicons to individuals. Subsequently, individuals are pooled equimolar and sequenced on the Ion Torrent next-generation sequencing platform. A bioinformatics pipeline identifies the alleles and recodes these to a genotypic format. Next, we test the utility of our markers. baps allocates the 84 crested newt individuals representing (candidate) species to their expected (candidate) species, confirming the markers are suitable for species delineation. newhybrids, a hybrid index and hiest confirm the 48 individuals from the presumed hybrid population to be genetically admixed, illustrating the potential of the markers to identify interspecific hybridization. We expect the set of markers we designed to provide a high resolving power for analysis of hybridization in Triturus. PMID:24571307

Wielstra, B; Duijm, E; Lagler, P; Lammers, Y; Meilink, W R M; Ziermann, J M; Arntzen, J W

2014-09-01

225

Exploring the distribution of genetic markers of pharmacogenomics relevance in Brazilian and Mexican populations.  

PubMed

Studies of pharmacogenomics-related traits are increasingly being performed to identify loci that affect either drug response or susceptibility to adverse drug reactions. However, the effect of the polymorphisms can differ in magnitude or be absent depending on the population being assessed. We used the Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus array to characterize the distribution of polymorphisms of pharmacogenetics and pharmacogenomics (PGx) relevance in two samples from the most populous Latin American countries, Brazil and Mexico. The sample from Brazil included 268 individuals from the southeastern state of Rio de Janeiro, and was stratified into census categories. The sample from Mexico comprised 45 Native American Zapotecas and 224 self-identified Mestizo individuals from 5 states located in geographically distant regions in Mexico. We evaluated the admixture proportions in the Brazilian and Mexican samples using a panel of Ancestry Informative Markers extracted from the DMET array, which was validated with genome-wide data. A substantial variation in ancestral proportions across census categories in Brazil, and geographic regions in Mexico was identified. We evaluated the extent of genetic differentiation (measured as FST values) of the genetic markers of the DMET Plus array between the relevant parental populations. Although the average levels of genetic differentiation are low, there is a long tail of markers showing large frequency differences, including markers located in genes belonging to the Cytochrome P450, Solute Carrier (SLC) and UDP-glucuronyltransferase (UGT) families as well as other genes of PGx relevance such as ABCC8, ADH1A, CHST3, PON1, PPARD, PPARG, and VKORC1. We show how differences in admixture history may have an important impact in the distribution of allele and genotype frequencies at the population level. PMID:25419701

Bonifaz-Peña, Vania; Contreras, Alejandra V; Struchiner, Claudio Jose; Roela, Rosimeire A; Furuya-Mazzotti, Tatiane K; Chammas, Roger; Rangel-Escareño, Claudia; Uribe-Figueroa, Laura; Gómez-Vázquez, María José; McLeod, Howard L; Hidalgo-Miranda, Alfredo; Parra, Esteban J; Fernández-López, Juan Carlos; Suarez-Kurtz, Guilherme

2014-01-01

226

Exploring the Distribution of Genetic Markers of Pharmacogenomics Relevance in Brazilian and Mexican Populations  

PubMed Central

Studies of pharmacogenomics-related traits are increasingly being performed to identify loci that affect either drug response or susceptibility to adverse drug reactions. However, the effect of the polymorphisms can differ in magnitude or be absent depending on the population being assessed. We used the Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus array to characterize the distribution of polymorphisms of pharmacogenetics and pharmacogenomics (PGx) relevance in two samples from the most populous Latin American countries, Brazil and Mexico. The sample from Brazil included 268 individuals from the southeastern state of Rio de Janeiro, and was stratified into census categories. The sample from Mexico comprised 45 Native American Zapotecas and 224 self-identified Mestizo individuals from 5 states located in geographically distant regions in Mexico. We evaluated the admixture proportions in the Brazilian and Mexican samples using a panel of Ancestry Informative Markers extracted from the DMET array, which was validated with genome-wide data. A substantial variation in ancestral proportions across census categories in Brazil, and geographic regions in Mexico was identified. We evaluated the extent of genetic differentiation (measured as FST values) of the genetic markers of the DMET Plus array between the relevant parental populations. Although the average levels of genetic differentiation are low, there is a long tail of markers showing large frequency differences, including markers located in genes belonging to the Cytochrome P450, Solute Carrier (SLC) and UDP-glucuronyltransferase (UGT) families as well as other genes of PGx relevance such as ABCC8, ADH1A, CHST3, PON1, PPARD, PPARG, and VKORC1. We show how differences in admixture history may have an important impact in the distribution of allele and genotype frequencies at the population level. PMID:25419701

Bonifaz-Peña, Vania; Contreras, Alejandra V.; Struchiner, Claudio Jose; Roela, Rosimeire A.; Furuya-Mazzotti, Tatiane K.; Chammas, Roger; Rangel-Escareño, Claudia; Uribe-Figueroa, Laura; Gómez-Vázquez, María José; McLeod, Howard L.; Hidalgo-Miranda, Alfredo

2014-01-01

227

Propylthiouracil tasting as a possible genetic association marker for two types of alcoholism.  

PubMed

The ability to taste 6-n-propylthiouracil (PROP) as bitter is determined genetically. The present study investigated whether this genetic ability was correlated with alcoholism and/or depression. Four groups of community college students (n = 25 each) were constituted based on the presence or absence of alcoholism and/or depression in themselves or their parents. Family history was assessed using the Family History-Research Diagnostic Criteria. Each subject was given a taste test using paper saturated with PROP. The results showed that subjects who had only alcoholism in their family were more likely to be nontasters of PROP than the control group, whereas subjects with both alcoholism and depression in their family were more likely to be so-called supertasters of PROP; that is, they found it extremely bitter. These findings suggest that PROP tasting might function as a genetic marker for two types of alcoholism. PMID:9662078

DiCarlo, S T; Powers, A S

1998-05-01

228

Population genetics of Schistosoma haematobium: development of novel microsatellite markers and their application to schistosomiasis control in Mali.  

PubMed

The recent implementation of mass drug administration (MDA) for control of uro-genital schistosomiasis has identified an urgent need for molecular markers to both directly monitor the impact of MDA, for example to distinguish re-infections from uncleared infections, as well as understand aspects of parasite reproduction and gene flow which might predict evolutionary change, such as the development and spread of drug resistance. We report the development of a novel microsatellite tool-kit allowing, for the first time, robust genetic analysis of individual S. haematobium larvae collected directly from infected human hosts. We genotyped the parasite populations of 47 children from 2 schools in the Ségou region of Mali, the first microsatellite study of this highly neglected parasite. There was only limited evidence of population subdivision between individual children or between the two schools, suggesting that few barriers to gene flow exist in this population. Complex relationships between parasite reproductive success, infection intensity and host age and gender were identified. Older children and boys harboured more diverse infections, as measured by the number of unique adult genotypes present. Individual parasite genotypes had variable reproductive success both across hosts, a pre-requisite for evolutionary selection, and, phenotypically, in hosts of different ages and genders. These data serve as a baseline against which to measure the effect of treatment on parasite population genetics in this region of Mali, and the tools developed are suitable to further investigate this important pathogen, and its close relatives, throughout their range. PMID:21679489

Gower, C M; Gabrielli, A F; Sacko, M; Dembelé, R; Golan, R; Emery, A M; Rollinson, D; Webster, J P

2011-07-01

229

An efficient method to find potentially universal population genetic markers, applied to metazoans  

PubMed Central

Background Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families. Results In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals. Conclusions Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa. PMID:20836842

2010-01-01

230

Development of Novel Simple Sequence Repeat Markers in Bitter Gourd (Momordica charantia L.) Through Enriched Genomic Libraries and Their Utilization in Analysis of Genetic Diversity and Cross-Species Transferability.  

PubMed

Microsatellite or simple sequence repeat (SSR) markers are the preferred markers for genetic analyses of crop plants. The availability of a limited number of such markers in bitter gourd (Momordica charantia L.) necessitates the development and characterization of more SSR markers. These were developed from genomic libraries enriched for three dinucleotide, five trinucleotide, and two tetranucleotide core repeat motifs. Employing the strategy of polymerase chain reaction-based screening, the number of clones to be sequenced was reduced by 81 % and 93.7 % of the sequenced clones contained in microsatellite repeats. Unique primer-pairs were designed for 160 microsatellite loci, and amplicons of expected length were obtained for 151 loci (94.4 %). Evaluation of diversity in 54 bitter gourd accessions at 51 loci indicated that 20 % of the loci were polymorphic with the polymorphic information content values ranging from 0.13 to 0.77. Fifteen Indian varieties were clearly distinguished indicative of the usefulness of the developed markers. Markers at 40 loci (78.4 %) were transferable to six species, viz. Momordica cymbalaria, Momordica subangulata subsp. renigera, Momordica balsamina, Momordica dioca, Momordica cochinchinesis, and Momordica sahyadrica. The microsatellite markers reported will be useful in various genetic and molecular genetic studies in bitter gourd, a cucurbit of immense nutritive, medicinal, and economic importance. PMID:25240849

Saxena, Swati; Singh, Archana; Archak, Sunil; Behera, Tushar K; John, Joseph K; Meshram, Sudhir U; Gaikwad, Ambika B

2015-01-01

231

Estimating black bear population density and genetic diversity at Tensas River, Louisiana using microsatellite DNA markers  

USGS Publications Warehouse

The Recovery Plan for the federally threatened Louisiana black bear (Ursus americanus luteolus) mandates that remnant populations be estimated and monitored. In 1999 we obtained genetic material with barbed-wire hair traps to estimate bear population size and genetic diversity at the 329-km2 Tensas River Tract, Louisiana. We constructed and monitored 122 hair traps, which produced 1,939 hair samples. Of those, we randomly selected 116 subsamples for genetic analysis and used up to 12 microsatellite DNA markers to obtain multilocus genotypes for 58 individuals. We used Program CAPTURE to compute estimates of population size using multiple mark-recapture models. The area of study was almost entirely circumscribed by agricultural land, thus the population was geographically closed. Also, study-area boundaries were biologically discreet, enabling us to accurately estimate population density. Using model Chao Mh to account for possible effects of individual heterogeneity in capture probabilities, we estimated the population size to be 119 (SE=29.4) bears, or 0.36 bears/km2. We were forced to examine a substantial number of loci to differentiate between some individuals because of low genetic variation. Despite the probable introduction of genes from Minnesota bears in the 1960s, the isolated population at Tensas exhibited characteristics consistent with inbreeding and genetic drift. Consequently, the effective population size at Tensas may be as few as 32, which warrants continued monitoring or possibly genetic augmentation.

Boersen, M.R.; Clark, J.D.; King, T.L.

2003-01-01

232

Comparison of algorithms to infer genetic population structure from unlinked molecular markers.  

PubMed

Identifying population genetic structure (PGS) is crucial for breeding and conservation. Several clustering algorithms are available to identify the underlying PGS to be used with genetic data of maize genotypes. In this work, six methods to identify PGS from unlinked molecular marker data were compared using simulated and experimental data consisting of multilocus-biallelic genotypes. Datasets were delineated under different biological scenarios characterized by three levels of genetic divergence among populations (low, medium, and high FST) and two numbers of sub-populations (K=3 and K=5). The relative performance of hierarchical and non-hierarchical clustering, as well as model-based clustering (STRUCTURE) and clustering from neural networks (SOM-RP-Q). We use the clustering error rate of genotypes into discrete sub-populations as comparison criterion. In scenarios with great level of divergence among genotype groups all methods performed well. With moderate level of genetic divergence (FST=0.2), the algorithms SOM-RP-Q and STRUCTURE performed better than hierarchical and non-hierarchical clustering. In all simulated scenarios with low genetic divergence and in the experimental SNP maize panel (largely unlinked), SOM-RP-Q achieved the lowest clustering error rate. The SOM algorithm used here is more effective than other evaluated methods for sparse unlinked genetic data. PMID:24964261

Peña-Malavera, Andrea; Bruno, Cecilia; Fernandez, Elmer; Balzarini, Monica

2014-08-01

233

A Comparison of Biallelic Markers and Microsatellites for the Estimation of Population and Conservation Genetic Parameters in Atlantic Salmon (Salmo salar)  

Microsoft Academic Search

Biallelic markers such as single nucleotide polymorphisms (SNPs) and insertion\\/deletion polymorphisms have become increasingly popular markers for various population genetics applications. However, the effort required to develop biallelic markers in nonmodel organisms is still substantial. In this study, we compared the estimation of various population genetic parameters (genetic divergence and structuring, isolation-by-distance, genetic diversity) using a limited number of biallelic

HEIKKI J. RYYNANEN; A NNI TONTERI; A NTI VASEMAGI; CRAIG R. PRIMMER

2007-01-01

234

Assessment of genetic diversity of wheat genotypes by resistance gene analog-EST markers.  

PubMed

Resistance gene analog-expressed sequence tag (RGA-EST)-based markers have been used for variety discrimination and studies of genetic diversity in wheat. Our aim is to increase the competitiveness of public wheat breeding programs through intensive use of modern selection technologies, mainly marker-assisted selection. The genetic diversity of 77 wheat nucleotide binding site (NBS)-containing RGA-ESTs was assessed. Resistant and susceptible bread wheat (Triticum aestivum) genotypes were used as sources of DNA for PCR amplifications. In our previous studies, the F? individuals derived from the combinations PI178383 x Harmankaya99, Izgi2001 x ES14, and Sonmez2001 x Aytin98 were evaluated for yellow rust resistance at both seedling and adult stages to identify DNA markers. We have now examined the genetic variability among the resistant and susceptible Turkish wheat cultivars for yellow rust disease and the mean genetic distance between the cultivars. The highest similarity was 0.500 between Harmankaya99 and Sonmez2001. The lowest similarity was 0.286 between Aytin98, PI178383 and Aytin98, ES14. A relatively high level (49.5%) of polymorphism was observed with 77 RGA-EST primers across the six wheat genotypes, despite the fact that all of them were local cultivars from geographically close locations. RGA-EST sequences were compared by BlastX algorithms for amino acid sequences to determine the polymorphic categories among the combinations. BlastX analyses of six RGA-ESTs that gave polymorphic patterns for all combinations were NBS-LRR class RGA, NB-ARC domain containing protein, NBS-type resistance protein RGC5, NBS-LRR-S/ TPK stem rust resistance protein, and putative MLA1 proteins, while 38 RGA-EST gave a monomorphic pattern. PMID:21710462

Karakas, O; Gurel, F; Uncuoglu, A A

2011-01-01

235

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing  

PubMed Central

The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus. PMID:25602379

Dasgupta, Modhumita Ghosh; Dharanishanthi, Veeramuthu; Agarwal, Ishangi; Krutovsky, Konstantin V.

2015-01-01

236

[Genetic analysis of mutant genes and RAPD marker of mutant gene of narrow leaflet in soybean].  

PubMed

Mutant E182 with "narrow leaflet-4 seeded pod" was selected from descendents of EMS-treated seeds of soybean variety Lu Dou No. 4 (LD4) with "ovate leaflet-without 4 seeded pod". Genetic analyses of F2 individuals of crossing between mutant E182 and parent LD4 indicated that segregation ratio between ovate and narrow leaflet was 3:1, so was segregation ratio between "without 4 seeded pod" and "4 seeded pod". Segregation ratios of four character types in F2 population of 1,654 individuals were beyond 9:3:3:1 of two pairs of independent gene, showing linkage inheritance. Reccmbinant ratio between mutant genes of narrow leaflet and 4 seeded pod was 11.24% +/- 0.81%. On the other hand, mutant E182, parent LD4 and F2, F3 individuals of their hybrids were analyzed by means of RAPD technique. The marker OPY6-1300 linked with the mutant gene of narrow leaflet was generated, and genetic distance of the marker and mutant gene was 8 cent Morgan (cM), being 10 cM nearer than RFLP marker of narrow leaflet generated by shoemaker. PMID:11209714

Zhu, B G; Bai, H X; Zhang, Y

2001-01-01

237

Risk Factors for HTLV-I Mother to Child Transmission: Influence of Genetic Markers.  

PubMed

This study was designed to evaluate the influence of genetic markers on the seropositivity of offspring of HTLV-I positive mothers in Tumaco, Colombia, an endemic area for HTLV-I infection and a site where there exists a racially mixed population of Black and Caucasian ancestors. 33 HTLV-I seropositive women with at least one offspring were studied. A total of 111 offspring were tested using hemaglutination-inhibition for testing sera for the allotypic markers G1m (1, 2, 3, 17) and G3m (5, 6, 13, 21). Potential risk factors such as mother s age at child's birth, mother's age at the time of the study, breastfeeding months, TSP vs. asymptomatic HTLV-I carrier, sibship's size, children's age and sex, were not found to be associated with mother to child transmission. Mother's Negroid genetic marker genotype (1, 17, 5, 13/1, 17, 5, +/- 13) was marginally associated with mother to child transmission of HTLV-I (P=0.0057; OR=11.97; CI=0.92-155.96) PMID:11103001

Arango; Rugeles; Concha; Borrero; Lai; Lai; Bernal; Bernal

1998-06-01

238

Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers  

Microsoft Academic Search

Recent development of DNA markers provides powerful tools for population genetic analyses. Amplified fragment length polymorphism (AFLP) markers result from a poly- merase chain reaction (PCR)-based DNA fingerprinting technique that can detect multiple restriction fragments in a single polyacrylamide gel, and thus are potentially useful for population genetic studies. Because AFLP markers have to be analysed as dominant loci in

G. Yan; J. Romero-Severson; M. Walton; D. D. CHADEEand; D. W. Severson

1999-01-01

239

Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar  

PubMed Central

Background The genus Nelumbo Adans. comprises two living species, N. nucifera Gaertan. (Asian lotus) and N. lutea Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop improvement but has not been generated for Nelumbo. We aimed to develop genomic simple sequence repeat (SSR) markers from the genome sequence and construct two genetic maps for Nelumbo to assist genome assembly and integration of a genetic map with the genome sequence. Results A total of 86,089 SSR motifs were identified from the genome sequences. Di- and tri-nucleotide repeat motifs were the most abundant, and accounted for 60.73% and 31.66% of all SSRs, respectively. AG/GA repeats constituted 51.17% of dinucleotide repeat motifs, followed by AT/TA (44.29%). Of 500 SSR primers tested, 386 (77.20%) produced scorable alleles with an average of 2.59 per primer, and 185 (37.00%) showed polymorphism among two parental genotypes, N. nucifera ‘Chinese Antique’ and N. lutea ‘AL1’, and six progenies of their F1 population. The normally segregating markers, which comprised 268 newly developed SSRs, 37 previously published SSRs and 53 sequence-related amplified polymorphism markers, were used for genetic map construction. The map for Asian lotus was 365.67 cM with 47 markers distributed in seven linkage groups. The map for American lotus was 524.51 cM, and contained 177 markers distributed in 11 genetic linkage groups. The number of markers per linkage group ranged from three to 34 with an average genetic distance of 3.97 cM between adjacent markers. Moreover, 171 SSR markers contained in linkage groups were anchored to 97 genomic DNA sequence contigs of ‘Chinese Antique’. The 97 contigs were merged into 60 scaffolds. Conclusion Genetic mapping of SSR markers derived from sequenced contigs in Nelumbo enabled the associated contigs to be anchored in the linkage map and facilitated assembly of the genome sequences of ‘Chinese Antique’. The present study reports the first construction of genetic linkage maps for Nelumbo, which can serve as reference linkage maps to accelerate characterization germplasm, genetic mapping for traits of economic interest, and molecular breeding with marker-assisted selection. PMID:23170872

2012-01-01

240

The Longue Durée of Genetic Ancestry: Multiple Genetic Marker Systems and Celtic Origins on the Atlantic Facade of Europe  

PubMed Central

Celtic languages are now spoken only on the Atlantic facade of Europe, mainly in Britain and Ireland, but were spoken more widely in western and central Europe until the collapse of the Roman Empire in the first millennium a.d. It has been common to couple archaeological evidence for the expansion of Iron Age elites in central Europe with the dispersal of these languages and of Celtic ethnicity and to posit a central European “homeland” for the Celtic peoples. More recently, however, archaeologists have questioned this “migrationist” view of Celtic ethnogenesis. The proposition of a central European ancestry should be testable by examining the distribution of genetic markers; however, although Y-chromosome patterns in Atlantic Europe show little evidence of central European influence, there has hitherto been insufficient data to confirm this by use of mitochondrial DNA (mtDNA). Here, we present both new mtDNA data from Ireland and a novel analysis of a greatly enlarged European mtDNA database. We show that mtDNA lineages, when analyzed in sufficiently large numbers, display patterns significantly similar to a large fraction of both Y-chromosome and autosomal variation. These multiple genetic marker systems indicate a shared ancestry throughout the Atlantic zone, from northern Iberia to western Scandinavia, that dates back to the end of the last Ice Age. PMID:15309688

McEvoy, Brian; Richards, Martin; Forster, Peter; Bradley, Daniel G.

2004-01-01

241

Genetic diversity and structure of farm and genebank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

The genetic diversity of 400 accessions collected in cacao farms, 95 genebank and 31 reference accessions was analyzed using 12 microsatelitte markers. The genebank and reference accessions were sub-divided into 12 accession groups (AG) that belong to the traditional cacao genetic groups (GG) Lower ...

242

Inter Simple Sequence Repeat (ISSR) Markers and Pedigree Information to Assess Genetic Diversity and Relatedness Within Raspberry Genotypes  

Microsoft Academic Search

Genetic diversity and relatedness among nine North American red raspberry (Rubus idaeus L.) cultivars and four Canadian breeding lines were studied using inter simple sequence repeat (ISSR) markers and pedigree analysis. Eighteen primers generated 306 polymorphic ISSR-PCR bands. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) revealed a substantial degree of genetic diversity among the 13 genotypes,

Samir C. Debnath

2008-01-01

243

Comparison of AFLP and SAMPL markers for assessment of intra-population genetic variation in Azadirachta indica A. Juss  

Microsoft Academic Search

Neem (Azadirachta indica) is an important tropical tree species with a number of medicinal and biopesticidal properties. In the present work, the extent of intra-population genetic variation was evaluated in neem accessions growing in district Kanpur (UP), India, along with two exotic accessions. Two PCR-based markers namely, AFLP and SAMPL were employed to measure the genetic variation. The relative efficiencies

A Singh; A Chaudhury; P. S Srivastava; M Lakshmikumaran

2002-01-01

244

Identification of Genetic Factors Contributing to Heterosis in a Hybrid From Two Elite Maize Inbred Lines Using Molecular Markers  

Microsoft Academic Search

The use of molecular markers to identify quantitative trait loci (QTLs) affecting agriculturally important traits has become a key approach in plant genetics-both for understanding the genetic basis of these traits and to help design novel plant improvement programs. In the study reported here, we mapped QTLs (and evaluated their phenotypic effects) associated with seven major traits (including grain yield)

Charles W. Stuber; Stephen E. Lincoln; David W. Wolff; Tim Helentjarisn; Eric S. Lander

245

Insertion-deletion polymorphisms (indels) as genetic markers in natural populations  

PubMed Central

Background We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations. Results Sequence reads from light shot-gun sequencing efforts of different dog breeds were aligned to the dog genome reference sequence and gaps corresponding to indels were identified. One hundred candidate markers (4-bp indels) were selected and genotyped in unrelated dogs (n = 7) and wolves (n = 18). Eighty-one and 76 out of 94 could be validated as polymorphic loci in the respective sample. Mean indel heterozygosity in a diverse set of wolves was 19%, and 74% of the loci had a minor allele frequency of >10%. Indels found to be polymorphic in wolves were subsequently genotyped in a highly bottlenecked Scandinavian wolf population. Fifty-one loci turned out to be polymorphic, showing their utility even in a population with low genetic diversity. In this population, individual heterozygosity measured at indel and microsatellite loci were highly correlated. Conclusion With an increasing amount of sequence information gathered from non-model organisms, we suggest that indels will come to form an important source of genetic markers, easy and cheap to genotype, for studies of natural populations. PMID:18211670

Väli, Ülo; Brandström, Mikael; Johansson, Malin; Ellegren, Hans

2008-01-01

246

Assessing genetic diversity in clonal organisms: low diversity or low resolution? Combining power and cost efficiency in selecting markers.  

PubMed

The increasing use of molecular tools to study populations of clonal organisms leads us to question whether the low polymorphism found in many studies reflects limited genetic diversity in populations or the limitations of the markers used. Here we used microsatellite datasets for two sea grass species to provide a combinatory statistic, combined with a likelihood approach to estimate the probability of identical multilocus genotypes (MLGs) to be shared by distinct individuals, in order to ascertain the efficiency of the markers used and to optimize cost-efficiently the choice of markers to use for deriving unbiased estimates of genetic diversity. These results strongly indicate that conclusions from studies on clonal organisms derived using markers showing low polymorphism, including microsatellites, should be reassessed using appropriate polymorphic markers. PMID:15743902

Arnaud-Haond, S; Alberto, F; Teixeira, S; Procaccini, G; Serrão, E A; Duarte, C M

2005-01-01

247

Population genetic structure of the tropical moss Acanthorrhynchium papillatum as measured with microsatellite markers.  

PubMed

Mosses and other bryophytes are vital components of forests, because they sustain a tremendous diversity of invertebrates and influence significant ecological functions. There have been few studies on moss population diversity in Southeast Asia, despite the escalating deforestation in this region of rich biodiversity. The genetic diversity of the tropical moss Acanthorrhynchium papillatum (Harv.) Fleisch., collected from forested areas in Singapore and Peninsular Malaysia, was elucidated using eight microsatellite markers developed for this species. Significant levels of allelic and haplotypic diversity were observed among clumps of the moss. Differences in allelic richness and genotypic diversity among the populations were higher in less disturbed forests compared to the more disturbed areas, suggesting that genetic diversity is affected by habitat quality. Genetic diversity levels within the clumps studied were low, indicating that vegetative reproduction was more important within clumps than sexual reproduction. However, multilocus genotypes of samples within the clumps studied were not all alike, providing evidence of microsatellite mutation or of occasional sexuality. Despite the isolation of populations, A. papillatum can introduce genetic variability by mutation among vegetatively propagated individuals. This study provides baseline information on the genetic diversity of A. papillatum tropical rain forests. PMID:22882300

Leonardía, A A P; Tan, B C; Kumar, P P

2013-03-01

248

A genetic historical sketch of European Gypsies: The perspective from autosomal markers.  

PubMed

In this study, 123 unrelated Portuguese Gypsies were analyzed for 15 highly polymorphic autosomal short tandem repeats (STRs). Average gene diversity across the 15 markers was 76.7%, which is lower than that observed in the non-Gypsy Portuguese population. Subsets of STRs were used to perform comparisons with other Gypsy and corresponding host populations. Interestingly, diversity reduction in Gypsy groups compared to their non-Gypsy surrounding populations apparently varied according to an East-West gradient, which parallels their dispersion in Europe as well as a decrease in complexity of their internal structure. Analysis of genetic distances revealed that the average level of genetic differentiation between Gypsy groups was much larger than that observed between the corresponding non-Gypsy populations. The high rate of heterogeneity among Gypsies can be explained by strong genetic drift and limited intergroup gene flow. However, when genetic relationships were addressed through principal component analysis, all Gypsy populations clustered together and was clearly distinguished from other populations, a pattern that suggests their common origin. Concerning the putative ancestral genetic component, admixture analysis did not reveal strong Indian ancestry in the current Gypsy gene pools, in contrast to the high admixture estimates for either Europeans or Western Asians. PMID:19918999

Gusmão, Alfredo; Valente, Cristina; Gomes, Verónica; Alves, Cíntia; Amorim, António; Prata, Maria João; Gusmão, Leonor

2010-04-01

249

Genetic linkage analysis of schizophrenia using chromosome 11q13-24 markers in Israeli pedigrees  

SciTech Connect

It is generally agreed that there is a genetic component in the etiology of schizophrenia which may be tested by the application of linkage analysis to multiply-affected families. One genetic region of interest is the long arm of chromosome 11 because of previously reported associations of genetic variation in this region with schizophrenia, and because of the fact that it contains the locus for the dopamine D2 receptor gene. In this study we have examined the segregation of schizophrenia with microsatellite dinucleotide repeat DNA markers along chromosome 11q in 5 Israeli families multiply-affected for schizophrenia. The hypothesis of linkage under genetic homogeneity of causation was tested under a number of genetic models. Linkage analysis provided no evidence for significant causal mutations within the region bounded by INT and D11S420 on chromosome 11q. It is still possible, however, that a gene of major effect exists in this region, either with low penetrance or with heterogeneity. 32 refs., 2 figs., 4 tabs.

Mulcrone, J.; Marchblanks, R.; Whatley, S.A. [Institute of Psychiatry, London (United Kingdom)] [and others

1995-04-24

250

Genetic diversity and structure of natural fragmented Chamaecyparis obtusa populations as revealed by microsatellite markers.  

PubMed

The genetic diversity and population structure of hinoki (Chamaecyparis obtusa) in Japan were investigated by examining the distribution of alleles at 13 microsatellite loci in 25 natural populations from Iwaki in northern Japan to Yakushima Island in southern Japan. On average, 26.9 alleles per locus were identified across all populations and 4.0% of the genetic variation was retained among populations (G(ST) = 0.040). According to linkage disequilibrium analysis, estimates of effective population size and detected evidence of bottleneck events, the genetic diversity of some populations may have declined as a result of fragmentation and/or over-exploitation. The central populations located in the Chubu district appear to have relatively large effective population sizes, while marginal populations, such as the Yakushima, Kobayashi and Iwaki populations, have smaller effective population sizes and are isolated from the other populations. Microsatellite analysis revealed the genetic uniqueness of the Yakushima population. Although genetic differentiation between populations was low, we detected a gradual cline in the genetic structure and found that locus Cos2619 may be non-neutral with respect to natural selection. PMID:20091205

Matsumoto, Asako; Uchida, Kohji; Taguchi, Yuriko; Tani, Naoki; Tsumura, Yoshihiko

2010-09-01

251

Assessment of genetic markers for species differentiation within the Mycobacterium tuberculosis complex.  

PubMed Central

It is important to correctly identify species within the Mycobacterium tuberculosis complex because of the zoonotic implications of bovine tuberculosis, especially in developing countries. We assessed the use of various genetic markers for species-specific identification of mycobacteria from the M. tuberculosis complex. A multiplex PCR designed for detection of the mtp40 and IS1081 elements was optimized and evaluated in 339 mycobacterial strains from different animal and geographic origins. The host range of the IS6110, MPB70, and 16S rRNA genes was also studied by PCR in all the strains. Finally, the usefulness of the genetic markers was compared by an immunoperoxidase test for specific identification of Mycobacterium bovis strains. The mtp40 sequence was detected in 87 of the 91 strains of M. tuberculosis and in 9 of the 11 Mycobacterium africanum strains but not in any of the M. bovis or Mycobacterium microti strains, indicating that the mtp40 element was also found in all of the M. tuberculosis complex strains isolated from seals. This organism is considered to be a true seal pathogen, but its origin is essentially unknown. The finding of the mtp40 element in the strains from seals suggests a closer relationship of these strains with a human origin than to an animal origin. The mtp40 element was not found in any other mycobacterial species included in the study. As a result of this study, we suggest that biochemical tests or alternate genetic markers are still needed to differentiate M. tuberculosis from M. africanum when these species coexist as causative agents of tuberculosis. The immunoperoxidase test worked well for the identification of M. bovis strains. We also report, for the first time, PCR amplification of the repetitive element IS6110 in an isolate of Mycobacterium ulcerans and an isolate of Mycobacterium gilvum, which emphasizes the need for further investigation of the host range of this sequence. PMID:8815111

Liébana, E; Aranaz, A; Francis, B; Cousins, D

1996-01-01

252

Genetic and demographic bottleneck analysis of Indian camel breeds by microsatellite markers.  

PubMed

The genetic and demographic bottleneck analysis of Indian camel breeds was carried out utilizing 40 microsatellite markers. Allelic polymorphism was observed at 20 loci in the Indian dromedary breeds. A total of 66 alleles were scored. The average number of alleles, expected heterozygosity and polymorphic information content were, respectively, 3.25?±?0.27, 0.56?±?0.04 and 0.49?±?0.04 in Bikaneri; 3.25?±?0.25, 0.53?±?0.03 and 0.46?±?0.03 in Jaisalmeri; 3.0?±?0.21, 0.53?±?0.04 and 0.45?±?0.03 in Kachchhi and 3.1?±?0.19, 0.51?±?0.03 and 0.44?±?0.03 in Mewari breed. Higher genetic variation was observed in most numerous Bikaneri breed. Genetic distances were least between the breed pair Bikaneri and Jaisalmeri which was closely placed with the Kachchhi breed. The Mewari camels had relatively higher genetic distance from the other three Indian dromedary breeds. The bottleneck analysis revealed the presence of genetic bottleneck in all four breeds of Indian dromedary. However, the qualitative graphical method resulted in normal L-shaped distribution of allele frequencies in Jaisalmeri breeds and shifted mode in Bikaneri, Kachchhi and Mewari breeds. The demographic bottleneck analysis revealed minimum reduction (-9.65 %) in the population of camels in Jaisalmeri breeding tract as compared to that of Bikaneri (-14.18 %), Kachchhi (-27.78 %) and Mewari (-32 %) breeding tracts. Conclusively, the genetic bottleneck analysis could explain the demographic bottleneck in the Indian dromedary populations. Therefore, appropriate conservation and improvement efforts are needed in all four dromedary breeds with immediate attention on Mewari and Kachchhi breeds. The present study is the first report in demonstrating the genetic basis of demographic bottleneck in the Indian dromedary populations. PMID:25134805

Mehta, Sharat Chandra

2014-12-01

253

Effect of diversity and missing data on genetic assignment with RAD-Seq markers.  

PubMed

Reduced representation libraries are being used as a preferred source of markers to address population genetic questions. However, libraries of RAD-Seq variants often suffer from significant percentage of missing data. In addition, algorithms used to mine SNPs from the raw data may also underscore biological variation. We investigate the effect of biological diversity in mining SNPs from the program STACKS and the effect of missing data on individual assignment implemented in STRUCTURE. We observed that changing diversity parameters in STACKS significantly alters the number of SNPs discovered and allowing for higher percentage of missing data retrieves more loci and possibly more power for individual assignment. PMID:25424532

Chattopadhyay, Balaji; Garg, Kritika M; Ramakrishnan, Uma

2014-01-01

254

Conservation genetics of Heritiera littoralis (Sterculiaceae), a threatened mangrove in China, based on AFLP and ISSR markers  

Microsoft Academic Search

AFLP and ISSR markers were used to determine the genetic variations in eight mangrove and non-mangrove populations of Heritiera littoralis (Sterculiaceae), a threatened species in China. Our results showed a moderate to high level of genetic variation in this species (P = 63.69%, HT = 0.20 for AFLP; P = 76.07%, HT = 0.22 for ISSR), and a relatively high level of genetic differentiation among populations (GST = 0.24 for

Shu-Guang Jian; Tian Tang; Yang Zhong; Su-Hua Shi

2010-01-01

255

The peopling of Greenland: further insights from the analysis of genetic diversity using autosomal and X-chromosomal markers.  

PubMed

The peopling of Greenland has a complex history shaped by population migrations, isolation and genetic drift. The Greenlanders present a genetic heritage with components of European and Inuit groups; previous studies using uniparentally inherited markers in Greenlanders have reported evidence of a sex-biased, admixed genetic background. This work further explores the genetics of the Greenlanders by analysing autosomal and X-chromosomal data to obtain deeper insights into the factors that shaped the genetic diversity in Greenlanders. Fourteen Greenlandic subsamples from multiple geographical settlements were compared to assess the level of genetic substructure in the Greenlandic population. The results showed low levels of genetic diversity in all sets of the genetic markers studied, together with an increased number of X-chromosomal loci in linkage disequilibrium in relation to the Danish population. In the broader context of worldwide populations, Greenlanders are remarkably different from most populations, but they are genetically closer to some Inuit groups from Alaska. Admixture analyses identified an Inuit component in the Greenlandic population of approximately 80%. The sub-populations of Ammassalik and Nanortalik are the least diverse, presenting the lowest levels of European admixture. Isolation-by-distance analyses showed that only 16% of the genetic substructure of Greenlanders is most likely to be explained by geographic barriers. We suggest that genetic drift and a differentiated settlement history around the island explain most of the genetic substructure of the population in Greenland. PMID:24801759

Pereira, Vania; Tomas, Carmen; Sanchez, Juan J; Syndercombe-Court, Denise; Amorim, António; Gusmão, Leonor; Prata, Maria João; Morling, Niels

2015-02-01

256

Genetic diversity of Tomistoma schlegelii inferred from mtDNA markers.  

PubMed

The genetic diversity of the endangered crocodile Tomistoma schlegelii was characterized using the protein coding ND 6-tRNA(glu)-cyt b and the cytochrome b-control region (cyt b-CR) markers. Concatenate data revealed six haplotypes with an overall haplotype diversity of 0.769 ± 0.039; nucleotide diversity was 0.00535 ± 0.00172. A nearest-neighbor analysis showed that all individuals clustered with four geographic regions (Sumatra, Peninsular Malaysia, Sarawak, and East Kalimantan) and were genetically differentiated. With the exception of the individuals from haplotype H2, which occurred in both Peninsular Malaysia and Sarawak, all other haplotypes were geographically distinct. The H4 lineage, which was found to be the most divergent, clustered exclusively in the basal clade in all phylogenetic trees, and the haplotype network was unconnected at the 95% reconnection limit, suggesting further investigation to establish its possible status as a distinct evolutionary significant unit or a cryptic species. PMID:23325482

Kaur, Taranjeet; Japning, Jeffrine Rovie Ryan; Sabki, Mohamad Shahbudin; Sidik, Irvan; Chong, Lee Kim; Ong, Alan H K

2013-04-01

257

Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers  

PubMed Central

Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of <5% were found in the landrace and modern variety gene pools, respectively, indicating greater numbers of rare variants, or likely new alleles, in landraces. Analysis of molecular variance (AMOVA) showed that A genome had the largest genetic differentiation and D genome the lowest. In contrast to genetic diversity, modern varieties displayed a wider average LD decay across the whole genome for locus pairs with r2>0.05 (P<0.001) than the landraces. Mean LD decay distance for the landraces at the whole genome level was <5 cM, while a higher LD decay distance of 5–10 cM in modern varieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5?25 cM) compared to landraces (<5?15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources. PMID:21365016

Hao, Chenyang; Wang, Lanfen; Ge, Hongmei; Dong, Yuchen; Zhang, Xueyong

2011-01-01

258

Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers  

PubMed Central

Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3? untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3? UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, “Stella” was separated from “Compact Stella.” This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3? UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry. PMID:22737155

Fernandez i Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font i Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

2012-01-01

259

Analysis of genetic diversity among Chinese wild Vitis species revealed with SSR and SRAP markers.  

PubMed

The genetic diversity among 80 Vitis materials including 62 indigenous accessions of 17 wild Vitis species in China and 7 interspecific hybrids, 10 V. vinifera L. cultivars, and 1 V. riparia Michaux were evaluated by simple sequence repeat and sequence-related amplified polymorphism markers. A total of 10 simple sequence repeat primers and 11 sequence-related amplified polymorphism primer combinations were amplified, and 260 bands were generated, of which 252 were polymorphic with an average polymorphism rate of 97.02%. Genetic relationships among the different Vitis species indicated that V. ficifolia and V. yeshanensis could be considered a separate species. As for the 4 major ecogeographic regions of Chinese wild Vitis species, the genetic diversities of Chinese wild Vitis species from the Qinling Mountain region (H = 0.1947, I = 0.3067) and the mid-downstream Yangtze River region (H = 0.1834, I = 0.2925) were higher, with results suggesting that these regions may be one of the major centers of Vitis origin. An understanding of the genetic diversity of these Chinese wild Vitis species could provide the theoretical foundation for further protection and reasonable utilization in grape breeding. PMID:23913379

Jing, Z B; Wang, X P; Cheng, J M

2013-01-01

260

Genetic variability in spotted seatrout (Cynoscion nebulosus), determined with microsatellite DNA markers  

USGS Publications Warehouse

Variation in the allele frequencies of five microsatellite loci was surveyed in 1256 individual spotted seatrout (Cynoscion nebulosus) obtained from 12 bays and estuaries from Laguna Madre, Texas, to Charlotte Harbor, Florida, to St. John's River on the Florida Atlantic Coast. Texas and Louisiana collection sites were resampled each year for two to four years (1998-2001). Genetic differentiation was observed. Spotted seatrout from Florida waters were strongly differentiated from spotted seatrout collected in Louisiana and Texas. The greatest genetic discontinuity was observed between Tampa Bay and Charlotte Harbor, and Charlotte Harbor seatrout were most similar to Atlantic Coast spotted seatrout. Texas and Louisiana samples were not strongly structured within the northwestern Gulf of Mexico and there was little evidence of temporal differentiation within bays. These findings are contrary to those of earlier analyses with allozymes and mitochondrial DNA (mtDNA) where evidence of spatial differentiation was found for spotted seatrout resident on the Texas coast. The differences in genetic structure observed among these markers may reflect differences in response to selective pressure, or may be due to differences in underlying genetic processes.

Ward, R.; Bowers, K.; Hensley, R.; Mobley, B.; Belouski, E.

2007-01-01

261

Association of Genetic Markers with CSF Oligoclonal Bands in Multiple Sclerosis Patients  

PubMed Central

Objective to explore the association between genetic markers and Oligoclonal Bands (OCB) in the Cerebro Spinal Fluid (CSF) of Italian Multiple Sclerosis patients. Methods We genotyped 1115 Italian patients for HLA-DRB1*15 and HLA-A*02. In a subset of 925 patients we tested association with 52 non-HLA SNPs associated with MS susceptibility and we calculated a weighted Genetic Risk Score. Finally, we performed a Genome Wide Association Study (GWAS) with OCB status on a subset of 562 patients. The best associated SNPs of the Italian GWAS were replicated in silico in Scandinavian and Belgian populations, and meta-analyzed. Results HLA-DRB1*15 is associated with OCB+: p?=?0.03, Odds Ratio (OR)?=?1.6, 95% Confidence Limits (CL)?=?1.1–2.4. None of the 52 non-HLA MS susceptibility loci was associated with OCB, except one SNP (rs2546890) near IL12B gene (OR: 1.45; 1.09–1.92). The weighted Genetic Risk Score mean was significantly (p?=?0.0008) higher in OCB+ (7.668) than in OCB? (7.412) patients. After meta-analysis on the three datasets (Italian, Scandinavian and Belgian) for the best associated signals resulted from the Italian GWAS, the strongest signal was a SNP (rs9320598) on chromosome 6q (p?=?9.4×10?7) outside the HLA region (65 Mb). Discussion genetic factors predispose to the development of OCB. PMID:23785401

Esposito, Federica; Lucenti, Ausiliatrice; Harbo, Hanne F.; Goris, An; Kockum, Ingrid; Oturai, Annette Bang; Celius, Elisabeth Gulowsen; Mero, Inger L.; Dubois, Bénédicte; Olsson, Tomas; Søndergaard, Helle Bach; Cusi, Daniele; Lupoli, Sara; Andreassen, Bettina Kulle; Myhr, Kjell-Morten; Guerini, Franca R.; Comi, Giancarlo

2013-01-01

262

Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes  

PubMed Central

Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm. PMID:21954370

Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

2011-01-01

263

Population genetics of Sargassum horneri (Fucales, Phaeophyta) in China revealed by ISSR and SRAP markers  

NASA Astrophysics Data System (ADS)

Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P % (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices ( F st) among the populations correlated well with their geographical distribution (Mantel test R =0.541 5, 0.541 8; P =0.005 0, 0.002 0 and R =0.728 6, 0.641 2; P =0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.

Yu, Shenhui; Chong, Zhuo; Zhao, Fengjuan; Yao, Jianting; Duan, Delin

2013-05-01

264

Comparisons of DNA marker-based genetic diversity with phenotypic estimates in maize grown in Pakistan.  

PubMed

We compared DNA-based genetic diversity estimates with conventional estimates by investigating agronomically important traits in maize grown in the northwestern region of Pakistan. RAPD markers were used to characterize 10 commonly cultivated maize genotypes. The same material was tested for phenotypic variation of quantitative traits using replicated field trials. The genetic distances between pairs of genotypes using RAPD data were used to generate a similarity matrix and to construct a phenogram. Statistical analyses were carried out on the data obtained from field trials of all maize genotypes for days to 50% tasseling, days to 50% silking, plant height, ear height, grain yield, grain weight per cob, and ear length. Analysis of variance and single degree of freedom contrasts were performed on morphological data to examine the relationship between molecular-based clusters and agronomic traits. A molecular marker-based phenogram led to the grouping of all genotypes into four major clusters, some of which were distantly related. These clusters contained one to four genotypes. Analysis of variance showed significant variations among all genotypes for agronomic traits. The single degree of freedom contrasts between groups of genotypes indicated significant differences for most traits. Pair-wise comparisons between clusters were also significant. The two types of data correlated well, providing an opportunity for better choices for selection. PMID:20882490

Shah, M M; Hassan, S W; Maqbool, K; Shahzadi, I; Pervez, A

2010-01-01

265

Miscanthus: genetic diversity and genotype identification using ISSR and RAPD markers.  

PubMed

Due to the limited number of molecular studies focused on European gene pool investigation, it is necessary to perform plant material recognition. Eighteen accessions of three Miscanthus species, namely, M. × giganteus, M. sinensis, M. sacchariflorus were evaluated with the use of molecular marker systems such as: inter simple sequence repeats (ISSRs), random amplified polymorphic DNA (RAPD), and by estimation of ploidy level based on flow cytometry. As a result, only one ISSR primer (ISSR1) and three RAPD primers (RAPD1, RAPD2, RAPD4) were required to identify all genotypes. Moreover, the use of the above mentioned molecular markers enable the proper species recognition of the interspecific hybrid M. × giganteus "Floridulus," which has been previously mislabeled as M. floridulus. The highest genetic similarity coefficient (0.94) was observed between M. × giganteus clones, which indicates that the genetic diversity within this species was very low. Whereas M. sinensis genotypes represented a relatively wide diversity with similarity coefficient of 0.58. Cluster analysis using UPGMA grouped the 18 accessions in three clusters according to species affiliation including relabeled M. × giganteus "Floridulus," which proved to be closely related to M.  × giganteus. Similar groupings were evident in the PCoA analysis. PMID:24880640

Cichorz, Sandra; Go?ka, Maria; Litwiniec, Anna

2014-10-01

266

A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers.  

PubMed

The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation. PMID:25146979

Santos, Sara; Oliveira, Manuela; Amorim, António; van Asch, Barbara

2014-11-01

267

Meta-analyses between 18 candidate genetic markers and overweight/obesity  

PubMed Central

Aims The goal of our study is to investigate the associations between 18 candidate genetic markers and overweight/obesity. Methods A total of 72 eligible articles were retrieved from literature databases including PubMed, Embase, SpingerLink, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Wanfang. Meta-analyses of 18 genetic markers among 56,738 controls and 48,148 overweight/obese persons were done by Review Manager 5.0. Results Our results showed that SH2B1 rs7498665 polymorphism was significantly associated with the risk of overweight/obesity (overall odds ratio (OR)?=?1.21, 95% confidence interval (CI)?=?1.09-1.34, P?=?0.0004). Increased risk of overweight/obesity was also observed in FAIM2 rs7138803 polymorphism (overall OR?=?1.11, 95% CI?=?1.01-1.22, P?=?0.04). Conclusion Our meta-analyses have shown the important role of 2 polymorphisms (SH2B1 rs7498665 and FAIM2 rs7138803) in the development of overweight/obesity. This study highlighted the importance of above two candidate genes (SH2B1 and FAIM2) in the risk of overweight/obesity. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2785487401176182. PMID:24621099

2014-01-01

268

Is there a genetic contribution to cultural differences? Collectivism, individualism and genetic markers of social sensitivity  

PubMed Central

Genes and culture are often thought of as opposite ends of the nature–nurture spectrum, but here we examine possible interactions. Genetic association studies suggest that variation within the genes of central neurotransmitter systems, particularly the serotonin (5-HTTLPR, MAOA-uVNTR) and opioid (OPRM1 A118G), are associated with individual differences in social sensitivity, which reflects the degree of emotional responsivity to social events and experiences. Here, we review recent work that has demonstrated a robust cross-national correlation between the relative frequency of variants in these genes and the relative degree of individualism–collectivism in each population, suggesting that collectivism may have developed and persisted in populations with a high proportion of putative social sensitivity alleles because it was more compatible with such groups. Consistent with this notion, there was a correlation between the relative proportion of these alleles and lifetime prevalence of major depression across nations. The relationship between allele frequency and depression was partially mediated by individualism–collectivism, suggesting that reduced levels of depression in populations with a high proportion of social sensitivity alleles is due to greater collectivism. These results indicate that genetic variation may interact with ecological and social factors to influence psychocultural differences. PMID:20592043

Lieberman, Matthew D.

2010-01-01

269

Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map  

PubMed Central

Background Triticale is adapted to a wide range of abiotic stress conditions, is an important high-quality feed stock and produces similar grain yield but more biomass compared to other crops. Modern genomic approaches aimed at enhancing breeding progress in cereals require high-quality genetic linkage maps. Consensus maps are genetic maps that are created by a joint analysis of the data from several segregating populations and different approaches are available for their construction. The phenomenon that alleles at a locus deviate from the Mendelian expectation has been defined as segregation distortion. The study of segregation distortion is of particular interest in doubled haploid (DH) populations due to the selection pressure exerted on the plants during the process of their establishment. Results The final consensus map, constructed out of six segregating populations derived from nine parental lines, incorporated 2555 DArT markers mapped to 2602 loci (1929 unique). The map spanned 2309.9 cM with an average number of 123.9 loci per chromosome and an average marker density of one unique locus every 1.2 cM. The R genome showed the highest marker coverage followed by the B genome and the A genome. In general, locus order was well maintained between the consensus linkage map and the component maps. However, we observed several groups of loci for which the colinearity was slightly uneven. Among the 2602 loci mapped on the consensus map, 886 showed distorted segregation in at least one of the individual mapping populations. In several DH populations derived by androgenesis, we found chromosomes (2B, 3B, 1R, 2R, 4R and 7R) containing regions where markers exhibited a distorted segregation pattern. In addition, we observed evidence for segregation distortion between pairs of loci caused either by a predominance of parental or recombinant genotypes. Conclusions We have constructed a reliable, high-density DArT marker consensus genetic linkage map as a basis for genomic approaches in triticale research and breeding, for example for multiple-line cross QTL mapping experiments. The results of our study exemplify the tremendous impact of different DH production techniques on allele frequencies and segregation distortion covering whole chromosomes. PMID:21798064

2011-01-01

270

Development of microsatellite markers and detection of genetic variation between Goniozus wasp populations.  

PubMed

Molecular genetic markers reveal differences between genotypes according to the presence of alleles (the same or different) at target loci. Microsatellite markers are especially useful co-dominant markers that have been used in a wide range of studies to elucidate the population structure and dynamics of a range of organisms, including agriculturally beneficial insects such as parasitic wasps (parasitoids). In the present study, twelve primer pairs were designed for the south Asian , Goniozus nephantidis (Muesebeck) (Hymenoptera: Bethylidae), and 24 for its New World congener, Goniozus legneri Gordh, parasitoids of the larvae of the lepidopteran coconut pest Opisina arenosella Walker (Lepidoptera: Crytophasidae) and other lepidopteran pests, respectively, in order to investigate polymorphism within and between populations. The wasps fingerprinted were a total of 85 G. nephantidis and G. legneri, including individuals belonging to three putatively different strains of G. legneri. Annealing gradient tests (50-65°C) were conducted to study the quality of the PCR amplification across an annealing temperature gradient using a mixed genotype DNA template from each species separately. Seven primer pairs, which amplified clear products of approximately the expected size of G. nephantidis and 18 of G. legneri, were then selected for capillary analysis for fragment size determination on a Beckmann CEQ 8000. Neither G. nephantidis nor G. legneri were polymorphic within populations. However, there were six primer pairs that did show polymorphism between G. legneri populations that originated from different geographical areas within South America (Uruguay and Chile). Furthermore, one primer pair revealed diversity between the two strains collected within Chile. One of the markers was subsequently used to provide unbiased assessment of primary sex ratio in G. legneri. PMID:25373190

Khidr, Sahand K; Hardy, Ian C W; Zaviezo, Tania; Mayes, Sean

2014-01-01

271

Development of Microsatellite Markers and Detection of Genetic Variation between Goniozus Wasp Populations  

PubMed Central

Molecular genetic markers reveal differences between genotypes according to the presence of alleles (the same or different) at target loci. Microsatellite markers are especially useful codominant markers that have been used in a wide range of studies to elucidate the population structure and dynamics of a range of organisms, including agriculturally beneficial insects such as parasitic wasps (parasitoids). In the present study, twelve primer pairs were designed for the south Asian , Goniozus nephantidis (Muesebeck) (Hymenoptera: Bethylidae), and 24 for its New World congener, Goniozus legneri Gordh, parasitoids of the larvae of the lepidopteran coconut pest Opisina arenosella Walker (Lepidoptera: Crytophasidae) and other lepidopteran pests, respectively, in order to investigate polymorphism within and between populations. The wasps fingerprinted were a total of 85 G. nephantidis and G. legneri, including individuals belonging to three putatively different strains of G. legneri. Annealing gradient tests (50–65°C) were conducted to study the quality of the PCR amplification across an annealing temperature gradient using a mixed genotype DNA template from each species separately. Seven primer pairs, which amplified clear products of approximately the expected size of G. nephantidis and 18 of G. legneri, were then selected for capillary analysis for fragment size determination on a Beckmann CEQ 8000. Neither G. nephantidis nor G. legneri were polymorphic within populations. However, there were six primer pairs that did show polymorphism between G. legneri populations that originated from different geographical areas within South America (Uruguay and Chile). Furthermore, one primer pair revealed diversity between the two strains collected within Chile. One of the markers was subsequently used to provide unbiased assessment of primary sex ratio in G. legneri. PMID:25373190

Khidr, Sahand K.; Hardy, Ian C.W.; Zaviezo, Tania; Mayes, Sean

2014-01-01

272

ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity  

Microsoft Academic Search

Drought, flood, salinity, or a combination of these limits rice production. Several rice varieties are well known for their\\u000a tolerance to specific abiotic stresses. We determined genetic relationship among 12 rice varieties including 9 tolerant to\\u000a drought, flood, or salinity using inter-simple sequence repeat (ISSR) markers. Based on all markers, the nine tolerant varieties\\u000a formed one cluster distinct from the

Ch Surendhar Reddy; A. Prasad Babu; B. P. Mallikarjuna Swamy; K. Kaladhar; N. Sarla

2009-01-01

273

Compatibility of pedigree-based and marker-based relationship matrices for single-step genetic evaluation  

PubMed Central

Background Single-step methods provide a coherent and conceptually simple approach to incorporate genomic information into genetic evaluations. An issue with single-step methods is compatibility between the marker-based relationship matrix for genotyped animals and the pedigree-based relationship matrix. Therefore, it is necessary to adjust the marker-based relationship matrix to the pedigree-based relationship matrix. Moreover, with data from routine evaluations, this adjustment should in principle be based on both observed marker genotypes and observed phenotypes, but until now this has been overlooked. In this paper, I propose a new method to address this issue by 1) adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix instead of the reverse and 2) extending the single-step genetic evaluation using a joint likelihood of observed phenotypes and observed marker genotypes. The performance of this method is then evaluated using two simulated datasets. Results The method derived here is a single-step method in which the marker-based relationship matrix is constructed assuming all allele frequencies equal to 0.5 and the pedigree-based relationship matrix is constructed using the unusual assumption that animals in the base population are related and inbred with a relationship coefficient ? and an inbreeding coefficient ??/?2. Taken together, this ? parameter and a parameter that scales the marker-based relationship matrix can handle the issue of compatibility between marker-based and pedigree-based relationship matrices. The full log-likelihood function used for parameter inference contains two terms. The first term is the REML-log-likelihood for the phenotypes conditional on the observed marker genotypes, whereas the second term is the log-likelihood for the observed marker genotypes. Analyses of the two simulated datasets with this new method showed that 1) the parameters involved in adjusting marker-based and pedigree-based relationship matrices can depend on both observed phenotypes and observed marker genotypes and 2) a strong association between these two parameters exists. Finally, this method performed at least as well as a method based on adjusting the marker-based relationship matrix. Conclusions Using the full log-likelihood and adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix provides a new and interesting approach to handle the issue of compatibility between the two matrices in single-step genetic evaluation. PMID:23206367

2012-01-01

274

Development of simple sequence repeat markers and the analysis of genetic diversity and ploidy level in a centipedegrass collection  

Technology Transfer Automated Retrieval System (TEKTRAN)

Little is known about the genetic variability of centipedegrass [Eremochloa ophiuroides (Munro) Hack] and few genetic tools have been available for this species. In this study, 69 unique Eremochloa sequences were generated by using a compound simple sequence repeat (SSR)-based cloning method. Twenty...

275

Inter and intra subpopulation genetic variability of roe deer (Capreolus capreolus L.) assessed by I and II class genetic markers.  

PubMed

The material was collected in three regions of Poland and consisted of 105 randomly chosen individuals killed during hunts (49 males, 56 females), out of which 51 were from Wielkopolska, 22 from Podkarpacie and 32 from Warmia. From each animal a blood sample was taken from the chest, stored in a probe with K2EDTA and frozen. The serum was used to establish the genotype for transferin and albumin whereas the samples with erythrocytes provided information on hemoglobin genotype. DNA was isolated from samples from each individual. Characteristics of eight (from among twelve studied) microsatellite loci and genetic distances were estimated by the use of standard computer package programs. Generally, monomorphism in blood proteins was registered. For the microsatellite loci the number of alleles ranged from 3 in the RT27-6-Fa locus (effectively two as the third allele was present only in two subpopulations with a very low frequency) to 10 in RT1-VI. Five loci showed heterozygosity of 0.5 or above which suggests their usefulness in parentage control. Considerable genetic distances (corresponding to geographical mileages) between the subpopulations were observed based on microsatellite markers. PMID:22195465

Kamieniarz, Robert; Wolc, Anna; Lisowski, Miros?aw; Dabert, Miros?awa; Grajewski, Bartosz; Steppa, Ryszard; Szwaczkowski, Tomasz

2011-01-01

276

Genetic structure and inter-generic relationship of closed colony of laboratory rodents based on RAPD markers.  

PubMed

Molecular genetic analysis was performed using random amplified polymorphic DNA (RAPD) on three commonly used laboratory bred rodent genera viz. mouse (Mus musculus), rat (Rattus norvegicus) and guinea pig (Cavia porcellus) as sampled from the breeding colony maintained at the Animal Facility, CSIR-Indian Institute of Toxicology Research, Lucknow. In this study, 60 samples, 20 from each genus, were analyzed for evaluation of genetic structure of rodent stocks based on polymorphic bands using RAPD markers. Thirty five random primers were assessed for RAPD analysis. Out of 35, only 20 primers generated a total of 56.88% polymorphic bands among mice, rats and guinea pigs. The results revealed significantly variant and distinct fingerprint patterns specific to each of the genus. Within-genera analysis, the highest (89.0%) amount of genetic homogeneity was observed in mice samples and the least (79.3%) were observed in guinea pig samples. The amount of genetic homogeneity was observed very high within all genera. The average genetic diversity index observed was low (0.045) for mice and high (0.094) for guinea pigs. The inter-generic distances were maximum (0.8775) between mice and guinea pigs; and the minimum (0.5143) between rats and mice. The study proved that the RAPD markers are useful as genetic markers for assessment of genetic structure as well as inter-generic variability assessments. PMID:25074272

Kumar, Mahadeo; Kumar, Sharad

2014-11-01

277

Genetic diversity and geographical differentiation of Iranian landrace, cultivars, and exotic chickpea lines as revealed by morphological and microsatellite markers.  

PubMed

Assessment of the extent of genetic variability within chickpea is fundamental for chickpea breeding and conservation of genetic resources and is particularly useful as a general guide in the choice of parents for breeding hybrids. To establish genetic diversity among 60 accessions of chickpea comprising landraces, internationally developed improved lines, and cultivars, genetic distances were evaluated using 14 simple sequence repeat markers. These markers showed a high level of polymorphism; a total of 59 different alleles were detected, with a mean of 4.2 alleles per locus. The polymorphic information content (PIC) value ranged from 0.31 to 0.89. All the markers, with the exception of TAA170, TA110, GA34, and Ts35, were considered to be informative (PIC?>?0.5), indicating their potential usefulness for cultivar identification. Based on the UNJ clustering method, all accessions were clustered in five groups, which indicated the probable origin and region similarity of Iranian landraces over the other cultivars. It also represents a wide diversity among available germplasm. The result has firmly established that introduction of genetic materials from exotic sources has broadened the genetic base of the national chickpea breeding program. As further implications of the findings, this study can be useful for selective breeding for specific traits and in enhancing the genetic base of breeding programs. PMID:24757326

Ghaffari, Parvin; Talebi, Reza; Keshavarzi, Fatemeh

2014-04-01

278

Dissecting the genetic make-up of North-East Sardinia using a large set of haploid and autosomal markers  

PubMed Central

Sardinia has been used for genetic studies because of its historical isolation, genetic homogeneity and increased prevalence of certain rare diseases. Controversy remains concerning the genetic substructure and the extent of genetic homogeneity, which has implications for the design of genome-wide association studies (GWAS). We revisited this issue by examining the genetic make-up of a sample from North-East Sardinia using a dense set of autosomal, Y chromosome and mitochondrial markers to assess the potential of the sample for GWAS and fine mapping studies. We genotyped individuals for 500K single-nucleotide polymorphisms, Y chromosome markers and sequenced the mitochondrial hypervariable (HVI–HVII) regions. We identified major haplogroups and compared these with other populations. We estimated linkage disequilibrium (LD) and haplotype diversity across autosomal markers, and compared these with other populations. Our results show that within Sardinia there is no major population substructure and thus it can be considered a genetically homogenous population. We did not find substantial differences in the extent of LD in Sardinians compared with other populations. However, we showed that at least 9% of genomic regions in Sardinians differed in LD structure, which is helpful for identifying functional variants using fine mapping. We concluded that Sardinia is a powerful setting for genetic studies including GWAS and other mapping approaches. PMID:22378280

Pardo, Luba M; Piras, Giovanna; Asproni, Rosanna; van der Gaag, Kristiaan J; Gabbas, Attilio; Ruiz-Linares, Andres; de Knijff, Peter; Monne, Maria; Rizzu, Patrizia; Heutink, Peter

2012-01-01

279

Genetic variability in maned wolf based on heterologous short-tandem repeat markers from domestic dog.  

PubMed

The maned wolf (Chrysocyon brachyurus) is the largest South American canid. Habitat loss and fragmentation, due to agricultural expansion and predatory hunting, are the main threats to this species. It is included in the official list of threatened wildlife species in Brazil, and is also protected by IUCN and CITES. Highly variable genetic markers such as microsatellites have the potential to resolve genetic relationships at all levels of the population structure (among individuals, demes or metapopulations) and also to identify the evolutionary unit for strategies for the conservation of the species. Tests were carried out to verify whether a class of highly polymorphic tetranucleotide repeats described for the domestic dog effectively amplifies DNA in the maned wolf. All five loci studied were amplified; however, one of these, was shown to be monomorphic in 69 maned wolf samples. The average allele number and estimated heterozygosity per polymorphic locus were 4.3 and 67%, respectively. The genetic variability found for this species, which is considered threatened with extinction, showed similar results when compared to studies of other canids. PMID:17624858

Salim, D C; Akimoto, A A; Carvalho, C B; Oliveira, S F; Grisolia, C K; Moreira, J R; Klautau-Guimarães, M N

2007-01-01

280

Genetic analysis of Sicilian autochthonous horse breeds using nuclear and mitochondrial DNA markers.  

PubMed

Genetic diversity and relationship among 3 Sicilian horse breeds were investigated using 16 microsatellite markers and a 397-bp length mitochondrial D-loop sequence. The analysis of autosomal DNA was performed on 191 horses (80 Siciliano [SIC], 61 Sanfratellano [SAN], and 50 Sicilian Oriental Purebred [SOP]). SIC and SAN breeds were notably higher in genetic variability than the SOP. Genetic distances and cluster analysis showed a close relationship between SIC and SAN breeds, as expected according to the breeds' history. Sequencing of hypervariable mitochondrial DNA region was performed on a subset of 60 mares (20 for each breed). Overall, 20 haplotypes with 31 polymorphic sites were identified: A higher haplotype diversity was detected in SIC and SAN breeds, with 13 and 11 haplotypes respectively, whereas only one haplotype was found in SOP. These were compared with 118 sequences from GenBank. BLAST showed that 17 of the 20 haplotypes had been reported previously in other breeds. One haplotype, found in SIC, traces back to a Bronze Age archaeological site (Inner Mongolia). The 3 Sicilian breeds are now rare, and 2 of them are officially endangered. Our results represent a valuable tool for management strategies as well as for conservation purposes. PMID:21914666

Guastella, Anna Maria; Zuccaro, Antonio; Criscione, Andrea; Marletta, Donata; Bordonaro, Salvatore

2011-01-01

281

Genetic structure of native circumpolar populations based on autosomal, mitochondrial, and Y chromosome DNA markers.  

PubMed

This study investigates the genetic structure of the present-day inhabitants of Beringia in order to answer questions concerning their origins and evolution. According to recent studies, the ancestors of Native Americans paused for a time in Beringia, during which they differentiated genetically from other Asians before peopling the New World. Furthermore, the Koryaks of Kamchatka share a "ubiquitous" allele (D9S1120) with Native Americans, indicating they may have descended from the same ancestral Beringian population that gave rise to the New World founders. Our results show that a genetic barrier exists between Kamchatkans (Koryaks and Even) and Bering Island inhabitants (Aleuts, mixed Aleuts, and Russians), based on Analysis of Molecular Variance (AMOVA) and structure analysis of nine autosomal short tandem repeats (STRs). This is supported by mitochondrial DNA evidence, but not by analysis of Y chromosome markers, as recent non-native male admixture into the region appears to have partially obscured ancient population relationships. Our study indicates that while Aleuts are descended from the original New World founders, the Koryaks are unlikely to represent a Beringian remnant of the ancestral population that gave rise to Native Americans. They are instead, like the Even, more recent arrivals to Kamchatka from interior Siberia, and the "ubiquitous" allele in Koryaks may result from recent gene flow from Chukotka. Genbank accession numbers for mtDNA sequences: GQ922935-GQ922973. PMID:20333712

Rubicz, Rohina; Melton, Phillip E; Spitsyn, Victor; Sun, Guangyun; Deka, Ranjan; Crawford, Michael H

2010-09-01

282

Interleukin-1 as a genetic marker for periodontitis: review of the literature.  

PubMed

Periodontitis is considered to be a multifactorial disease. Studies have indicated that part of the clinical variability in periodontitis may be explained by genetic factors. Genes can affect the immunoinflammatory host response to bacterial challenge in the periodontal tissues by means of an overproduction of proinflammatory cytokines, such as interleukin-1 (IL-1). IL-1 plays an important role in the pathogenesis of periodontitis, through its involvement in the regulation of the host's inflammatory response and bone resorption. Therefore, the genes that encode for IL-1 production have recently received most attention as potential predictors of periodontal disease progression. Hence, the relationship between IL-1 genotype and periodontal disease has been investigated by a number of studies. This review article aimed to determine whether IL-1 could be regarded as a genetic marker for periodontitis by reviewing data concerning susceptibility, clinical parameters, and treatment strategies in relation to the IL-1 genotype. The review concluded that there is currently limited evidence to implicate a specific IL-1 genotype as a risk factor for chronic periodontitis in white populations. However, there is limited evidence that genetic variation in the IL-1B polymorphism could be a risk factor for aggressive periodontitis. PMID:20490394

Grigoriadou, Marianna E; Koutayas, Spiridon-Oumvertos; Madianos, Phoebus N; Strub, Jorg-Rudolf

2010-06-01

283

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers  

PubMed Central

Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest. PMID:23036012

2012-01-01

284

Unique chromosome behavior and genetic control in Brassica × Orychophragmus wide hybrids: a review  

Microsoft Academic Search

Researchers recognized early that chromosome behavior, as other morphological characters, is under genetic control and gave\\u000a some cytogenetical examples such as the homoeologous chromosome pairing in wheat. In the intergeneric sexual hybrids between\\u000a cultivated Brassica species and another crucifer Orychophragmus violaceus, the phenomenon of parental genome separation was found under genetic control during mitosis and meiosis. The cytogenetics\\u000a of these

Zai-yun Li; Xian-hong Ge

2007-01-01

285

Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers  

PubMed Central

Background Alfalfa (Medicago sativa) is a major forage crop. The genetic progress is slow in this legume species because of its autotetraploidy and allogamy. The genetic structure of this species makes the construction of genetic maps difficult. To reach this objective, and to be able to detect QTLs in segregating populations, we used the available codominant microsatellite markers (SSRs), most of them identified in the model legume Medicago truncatula from EST database. A genetic map was constructed with AFLP and SSR markers using specific mapping procedures for autotetraploids. The tetrasomic inheritance was analysed in an alfalfa mapping population. Results We have demonstrated that 80% of primer pairs defined on each side of SSR motifs in M. truncatula EST database amplify with the alfalfa DNA. Using a F1 mapping population of 168 individuals produced from the cross of 2 heterozygous parental plants from Magali and Mercedes cultivars, we obtained 599 AFLP markers and 107 SSR loci. All but 3 SSR loci showed a clear tetrasomic inheritance. For most of the SSR loci, the double-reduction was not significant. For the other loci no specific genotypes were produced, so the significant double-reduction could arise from segregation distortion. For each parent, the genetic map contained 8 groups of four homologous chromosomes. The lengths of the maps were 2649 and 3045 cM, with an average distance of 7.6 and 9.0 cM between markers, for Magali and Mercedes parents, respectively. Using only the SSR markers, we built a composite map covering 709 cM. Conclusions Compared to diploid alfalfa genetic maps, our maps cover about 88–100% of the genome and are close to saturation. The inheritance of the codominant markers (SSR) and the pattern of linkage repulsions between markers within each homology group are consistent with the hypothesis of a tetrasomic meiosis in alfalfa. Except for 2 out of 107 SSR markers, we found a similar order of markers on the chromosomes between the tetraploid alfalfa and M. truncatula genomes indicating a high level of colinearity between these two species. These maps will be a valuable tool for alfalfa breeding and are being used to locate QTLs. PMID:14683527

Julier, Bernadette; Flajoulot, Sandrine; Barre, Philippe; Cardinet, Gaëlle; Santoni, Sylvain; Huguet, Thierry; Huyghe, Christian

2003-01-01

286

Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers  

Microsoft Academic Search

Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for\\u000a the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity\\u000a in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from\\u000a single nucleotide polymorphism (SNP)

Delphine Van InghelandtAlbrecht; Albrecht E. Melchinger; Claude Lebreton; Benjamin Stich

2010-01-01

287

A study of genetic diversity of sesame ( Sesamum indicum L.) in Vietnam and Cambodia estimated by RAPD markers  

Microsoft Academic Search

Sesame (Sesamum indicum L.) is a traditional oil crop cultivated throughout South East Asia. To estimate the genetic diversity of this crop in parts\\u000a at the region, 22 sesame accessions collected in Vietnam and Cambodia were analyzed using 10 RAPD markers. The 10 primers\\u000a generated 107 amplification products of which 88 were polymorphic fragments (83%). Genetic diversity of all populations

Toan Duc Pham; Tri Minh Bui; Gun Werlemark; Tuyen Cach Bui; Arnulf Merker; Anders S. Carlsson

2009-01-01

288

Evaluation of genetic diversity in Turkish melons ( Cucumis melo L.) based on phenotypic characters and RAPD markers  

Microsoft Academic Search

The genetic relationships among 56 melon (Cucumis melo L.) genotypes collected from various parts of Turkey were determined by comparing their phenotypic and molecular traits with\\u000a those of 23 local and foreign melon genotypes to investigate the taxonomic relationships and genetic variation of Turkish\\u000a melon germplasm. Sixty-one phenotypic characters and 109 polymorphic RAPD markers obtained from 33 primers were used

Suat Sensoy; Saadet Büyükalaca; Kazim Abak

2007-01-01

289

Effects of reforestation methods on genetic diversity of lodgepole pine: an assessment using microsatellite and randomly amplified polymorphic DNA markers  

Microsoft Academic Search

We examined the effects of different methods of forest regeneration on the genetic diversity of lodgepole pine (Pinus contorta var ‘latifolia’) using two different DNA-based molecular markers [randomly amplified polymorphic DNA (RAPDs) and microsatellites\\u000a or simple sequence repeats (SSRs)]. Genetic diversity was estimated for 30 individuals in each of four populations for the\\u000a following three stand types: (1)?mature lodgepole pine

B. R. Thomas; S. E. Macdonald; M. Hicks; D. L. Adams; R. B. Hodgetts

1999-01-01

290

[Analysis of genetic diversity on 9 wild stocks of taimen (Hucho taimen) by microsatellite markers].  

PubMed

Taimen (Hucho taimen) is a native fish species in China and it is in the state of endangerment. To explain clearly the genetic diversity and genetic structure, 9 wild populations of taimen were investigated using 20 microsatellite markers. The results showed that their observed heterozygosity ranged from 0.0994 to 0.8882, the expected heterozygosity varied from 0.2005 to 0.8759, and the range of PIC index was from 0.3432 to 0.5261 while population from Huma River had low genetic diversity. Fst of matching group ranged from 0.0246 to 0.2333 (P <0.0001)and Nm varied among 0.8216 to 9.9292, which indicated that the genetic differentiation was remarkable among populations.The half/full-sib family tests detected a proportion of half/full-sib family groups varying among 27.78% to 90.91%, showing a high inbred pressure and a risk of bottlenecks experienced by most groups. The AMOVA results showed that the global Fst was 0.1081; the clustering result showed that individuals from Beiji tributary of Heilongjiang River clustered as one clade, all individuals from Huma River and Wusuli River clustered as one clade and all individuals from the upper reaches of the Heilongjiang River clustered as another clade. All these results indicated that the decrease of taimen resource has affected the gene exchange among their populations. In order to achieve full protection of taimen germplasm resources, we should put an end to the destructive fishing for taimen and promotegene exchange among their populations. PMID:22184017

Liu, Bo; Kuang, You-Yi; Tong, Guang-Xiang; Yin, Jia-Sheng

2011-12-01

291

Genetic Markers of Co-Morbid Depression and Alcoholism in Women  

PubMed Central

Background Alcohol Dependence (AD) is often accompanied by co-morbid depression. Recent clinical evidence supports the benefit of subtype specific pharmacotherapy in treating the population of AD subjects with co-morbid major depressive disorder (MDD). However, in many AD subjects, depression is a reactive response to chronic alcohol use and withdrawal, and abates with a period of abstinence. Genetic markers may distinguish alcohol dependent subjects with MDD not tied chronologically and etiologically to their alcohol consumption. In this work we investigated the association of adenylyl cyclase genes (ADCY1–9), which are implicated in both AD and mood disorders, with alcoholism and co-morbid depression. Methods Subjects from Vienna, Austria (n = 323) were genotyped and SNPs (1,152) encompassing the genetic locations of the nine ADCY genes were examined. The Vienna cohort contained alcohol dependent subjects differentiated using the Lesch Alcoholism Typology. In this typology subjects are segregated into four types. Type III alcoholism is distinguished by co-occurrence of symptoms of depression and by affecting predominantly females. Results We identified four haplotypes associated with the phenotype of Type III alcoholism in females. One haplotype was in a genomic area in proximity to ADCY2, but actually within a lincRNA gene, two haplotypes were within ADCY5, and one haplotype was within the coding region of ADCY8. Three of the four haplotypes contributed independently to Type III alcoholism and together generated a positive predictive value of 72% and a negative predictive value of 78% for distinguishing women with a Lesch Type III diagnosis versus women designated as Type I or II alcoholics. Conclusions Polymorphisms in ADCY8 and ADCY5 and within a lincRNA are associated with an AD phenotype in females, which is distinguished by co-morbid signs of depression. Each of these genetic locations can rationally contribute to the polygenic etiology of the alcoholism/depression phenotype and the use of these genetic markers may aid in choosing appropriate and beneficial treatment strategies. PMID:23278386

Procopio, Daniela O.; Saba, Laura M.; Walter, Henriette; Lesch, Otto; Skala, Katrin; Schlaff, Golda; Vanderlinden, Lauren; Clapp, Peter; Hoffman, Paula L.; Tabakoff, Boris

2012-01-01

292

Molecular cloning and characterisation of the RESA gene, a marker of genetic diversity of Plasmodium falciparum  

PubMed Central

To identity immunodiagnostic antigen genes, a Plasmodium falciparum (Dd2 clone) expression library was screened using human immune sera. The ring-infected erythrocyte surface antigen (RESA) was isolated: this antigen of the resistant clone presents repeat tandem sequences like the 3D7 clone, albeit in different numbers. RESA has been studied as a marker of genetic diversity, with different sizes being observed in different isolates and clones of Plasmodium falciparum. The native protein was localised in cultures by western-blot and immuno-transmission electron microscopy. The antigenicity of RESA was evaluated by ELISA, using the carboxy-terminal repeat region as antigen. The assay’s sensitivity and specificity were 78.2 and 94% respectively. PMID:19816792

Moyano, Eva M.; González, Luis Miguel; Cuevas, Laureano; Perez-Pastrana, Esperanza; Santa-Maria, Ysmael

2009-01-01

293

Genetic ancestry inference using support vector machines, and the active emergence of a unique American population.  

PubMed

We use genotype data from the Marshfield Clinical Research Foundation Personalized Medicine Research Project to investigate genetic similarity and divergence between Europeans and the sampled population of European Americans in Central Wisconsin, USA. To infer recent genetic ancestry of the sampled Wisconsinites, we train support vector machines (SVMs) on the positions of Europeans along top principal components (PCs). Our SVM models partition continent-wide European genetic variance into eight regional classes, which is an improvement over the geographically broader categories of recent ancestry reported by personal genomics companies. After correcting for misclassification error associated with the SVMs (<10%, in all cases), we observe a >14% discrepancy between insular ancestries reported by Wisconsinites and those inferred by SVM. Values of FST as well as Mantel tests for correlation between genetic and European geographic distances indicate minimal divergence between Europe and the local Wisconsin population. However, we find that individuals from the Wisconsin sample show greater dispersion along higher-order PCs than individuals from Europe. Hypothesizing that this pattern is characteristic of nascent divergence, we run computer simulations that mimic the recent peopling of Wisconsin. Simulations corroborate the pattern in higher-order PCs, demonstrate its transient nature, and show that admixture accelerates the rate of divergence between the admixed population and its parental sources relative to drift alone. Together, empirical and simulation results suggest that genetic divergence between European source populations and European Americans in Central Wisconsin is subtle but already under way. PMID:23211701

Haasl, Ryan J; McCarty, Catherine A; Payseur, Bret A

2013-05-01

294

Genetic Variability among Lucerne Cultivars Based on Biochemical (SDS-PAGE) and Morphological Markers  

NASA Astrophysics Data System (ADS)

The present research was conducted to determine the genetic variability of 18 Lucerne cultivars, based on morphological and biochemical markers. The traits studied were plant height, tiller number, biomass, dry yield, dry yield/biomass, dry leaf/dry yield, macro and micro elements, crude protein, dry matter, crude fiber and ash percentage and SDS- PAGE in seed and leaf samples. Field experiments included 18 plots of two meter rows. Data based on morphological, chemical and SDS-PAGE markers were analyzed using SPSSWIN soft ware and the multivariate statistical procedures: cluster analysis (UPGMA), principal component. Analysis of analysis of variance and mean comparison for morphological traits reflected significant differences among genotypes. Genotype 13 and 15 had the greatest values for most traits. The Genotypic Coefficient of Variation (GCV), Phenotypic Coefficient of Variation (PCV) and Heritability (Hb) parameters for different characters raged from 12.49 to 26.58% for PCV, hence the GCV ranged from 6.84 to 18.84%. The greatest value of Hb was 0.94 for stem number. Lucerne genotypes could be classified, based on morphological traits, into four clusters and 94% of the variance among the genotypes was explained by two PCAs: Based on chemical traits they were classified into five groups and 73.492% of variance was explained by four principal components: Dry matter, protein, fiber, P, K, Na, Mg and Zn had higher variance. Genotypes based on the SDS-PAGE patterns all genotypes were classified into three clusters. The greatest genetic distance was between cultivar 10 and others, therefore they would be suitable parent in a breeding program.

Farshadfar, M.; Farshadfar, E.

295

Genomic Selection for Adjacent Genetic Markers of Yorkshire Pigs Using Regularized Regression Approaches  

PubMed Central

This study considers a problem of genomic selection (GS) for adjacent genetic markers of Yorkshire pigs which are typically correlated. The GS has been widely used to efficiently estimate target variables such as molecular breeding values using markers across the entire genome. Recently, GS has been applied to animals as well as plants, especially to pigs. For efficient selection of variables with specific traits in pig breeding, it is required that any such variable selection retains some properties: i) it produces a simple model by identifying insignificant variables; ii) it improves the accuracy of the prediction of future data; and iii) it is feasible to handle high-dimensional data in which the number of variables is larger than the number of observations. In this paper, we applied several variable selection methods including least absolute shrinkage and selection operator (LASSO), fused LASSO and elastic net to data with 47K single nucleotide polymorphisms and litter size for 519 observed sows. Based on experiments, we observed that the fused LASSO outperforms other approaches. PMID:25358359

Park, Minsu; Kim, Tae-Hun; Cho, Eun-Seok; Kim, Heebal; Oh, Hee-Seok

2014-01-01

296

Genomic selection for adjacent genetic markers of yorkshire pigs using regularized regression approaches.  

PubMed

This study considers a problem of genomic selection (GS) for adjacent genetic markers of Yorkshire pigs which are typically correlated. The GS has been widely used to efficiently estimate target variables such as molecular breeding values using markers across the entire genome. Recently, GS has been applied to animals as well as plants, especially to pigs. For efficient selection of variables with specific traits in pig breeding, it is required that any such variable selection retains some properties: i) it produces a simple model by identifying insignificant variables; ii) it improves the accuracy of the prediction of future data; and iii) it is feasible to handle high-dimensional data in which the number of variables is larger than the number of observations. In this paper, we applied several variable selection methods including least absolute shrinkage and selection operator (LASSO), fused LASSO and elastic net to data with 47K single nucleotide polymorphisms and litter size for 519 observed sows. Based on experiments, we observed that the fused LASSO outperforms other approaches. PMID:25358359

Park, Minsu; Kim, Tae-Hun; Cho, Eun-Seok; Kim, Heebal; Oh, Hee-Seok

2014-12-01

297

Crystal structure of human esterase D: a potential genetic marker of retinoblastoma  

SciTech Connect

Retinoblastoma (RB), a carcinoma of the retina, is caused by mutations in the long arm of chromosome 13, band 13q14. The esterase D (ESD) gene maps at a similar location as the RB gene locus and therefore serves as a potential marker for the prognosis of retinoblastoma. Because very little is known about the structure and function of ESD, we determined the 3-dimensional structure of the enzyme at 1.5 {angstrom} resolution using X-ray crystallography. ESD shows a single domain with an {alpha}/{beta}-hydrolase fold. A number of insertions are observed in the canonical {alpha}/{beta}-hydrolase fold. The active site is located in a positively charged, shallow cleft on the surface lined by a number of aromatic residues. Superimposition studies helped identify the typical catalytic triad residues -- Ser-153, His264, and Asp230 -- involved in catalysis. Mutagenesis of any of the catalytic triad residues to alanine abolished the enzyme activity. Backbone amides of Leu54 and Met150 are involved in the formation of the oxyanion hole. Interestingly, a M150A mutation increased the enzyme activity by 62%. The structure of human ESD determined in this study will aid the elucidation of the physiological role of the enzyme in the human body and will assist in the early diagnosis of retinoblastoma. Wu, D., Li, Y., Song, G., Zhang, D., Shaw, N., Liu, Z. J. Crystal structure of human esterase D: a potential genetic marker of retinoblastoma.

Wu, Dong; Li, Yang; Song, Gaojie; Zhang, David; Shaw, Neil; Liu, Zhi-Jie; (Chinese Aca. Sci.)

2009-07-10

298

Unexpected Genetic Diversity among and within Populations of the Toxic Dinoflagellate Alexandrium catenella as Revealed by Nuclear Microsatellite Markers?  

PubMed Central

Since 1998, blooms of Alexandrium catenella associated with paralytic shellfish poisoning have been repeatedly reported for Thau Lagoon (French Mediterranean coast). Based on data obtained for rRNA gene markers, it has been suggested that the strains involved could be closely related to the Japanese temperate Asian ribotype of the temperate Asian clade. In order to gain more insight into the origin of these organisms, we carried out a genetic analysis of 61 Mediterranean and 23 Japanese strains using both ribosomal and microsatellite markers. Whereas the phylogeny based on ribosomal markers tended to confirm the previous findings, the analysis of microsatellite sequences revealed an unexpected distinction between the French and Japanese populations. This analysis also highlighted great intraspecific diversity that was not detected with the classical rRNA gene markers. The Japanese strains are divided into two differentiated A. catenella lineages: the Sea of Japan lineage and the east coast lineage, which includes populations from the Inland Sea and the Pacific Ocean. A. catenella strains isolated from Thau Lagoon belong to another lineage. These findings indicate that microsatellite markers are probably better suited to investigations of the population genetics of this species that is distributed worldwide. Finally, application of the population genetics concepts available for macroorganisms could support new paradigms for speciation and migration in phytoplankton assemblages. PMID:19201972

Masseret, Estelle; Grzebyk, Daniel; Nagai, Satoshi; Genovesi, Benjamin; Lasserre, Bernard; Laabir, Mohamed; Collos, Yves; Vaquer, André; Berrebi, Patrick

2009-01-01

299

A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa.  

PubMed Central

A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an F(2) population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene analogs, covering 513 cM. In the case of EST-based markers we used an intron-targeted marker strategy with primers designed to anneal in conserved exon regions and to amplify across intron regions. Polymorphisms were significantly more frequent in intron vs. exon regions, thus providing an efficient mechanism to map transcribed genes. Genetic and cytogenetic analysis produced eight well-resolved linkage groups, which have been previously correlated with eight chromosomes by means of FISH with mapped BAC clones. We anticipated that mapping of conserved coding regions would have utility for comparative mapping among legumes; thus 60 of the EST-based primer pairs were designed to amplify orthologous sequences across a range of legume species. As an initial test of this strategy, we used primers designed against M. truncatula exon sequences to rapidly map genes in M. sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar and establishes the basis for a Medicago composite map. PMID:15082563

Choi, Hong-Kyu; Kim, Dongjin; Uhm, Taesik; Limpens, Eric; Lim, Hyunju; Mun, Jeong-Hwan; Kalo, Peter; Penmetsa, R Varma; Seres, Andrea; Kulikova, Olga; Roe, Bruce A; Bisseling, Ton; Kiss, Gyorgy B; Cook, Douglas R

2004-01-01

300

Using Random Sequence Primers in the Polymerase Chain Reaction to identify Gender-Specific Genetic Markers in House Wrens  

Microsoft Academic Search

In order to fully understand the biology of asexually reproducing organism, it is essential that one is able to distinguish the males from the females. In determining the gender of monomorphic birds, standard techniques including visual identification, surgery, and karyotyping are impossible or impractical for large-scale studies. A reliable gender identification method that uses genetic markers identified within the DNA

Jeremy J. Kirchman

1994-01-01

301

M A J O R A R T I C L E Genetic Diversity as a Marker for Timing  

E-print Network

M A J O R A R T I C L E Genetic Diversity as a Marker for Timing Infection in HIV-Infected Patients resistance surveillance specimens may be used to classify the duration of HIV infection as 1 year. We describe a mixed base classifier (MBC) optimized to categorize the duration of subtype B infections as

Aris-Brosou, Stéphane

302

Using microsatellite DNA markers to determine the genetic identity of parental clones used in the Louisiana sugarcane breeding program  

Technology Transfer Automated Retrieval System (TEKTRAN)

Sugarcane propagates asexually through vegetative cuttings. To validate the genetic identity of sugarcane clones during shipping and handling, we produced molecular fingerprints based on 21 microsatellite (SSR) DNA markers for 116 Louisiana parental clones that were included in the crossing program...

303

Osteopontin: an early innate immune marker of Escherichia coli mastitis harbors genetic polymorphisms with possible links with resistance to mastitis  

Microsoft Academic Search

BACKGROUND: Mastitis is the most important disease in dairy cows and it causes significant lost of profit to producers. Identification of the genes, and their variants, involved in innate immune responses is essential for the understanding of this inflammatory disease and to identify potential genetic markers for resistance to mastitis. The progeny of dairy cows would benefit from receiving favourable

Karin Alain; Niel A Karrow; Catherine Thibault; Jessika St-Pierre; Martin Lessard; Nathalie Bissonnette

2009-01-01

304

Assessing genetic diversity and its changes of bread wheat in Qinghai Province, China, using agronomic traits and microsatellite markers  

Microsoft Academic Search

Little is known about the diversity of wheat in Qinghai Province, China. Agronomic traits and microsatellite markers were used to survey genetic diversity and its change with time in 66 wheat cultivars registered from 1957 to 2009 in Qinghai Province. The average values of plant height, ear length, spikelets per ear, effective spikelets per ear, effective tillers per plant, internode

Hong-qin Li; Huai-gang Zhang; Bao-long Liu; Deng-cai Liu; Bo Zhang

2012-01-01

305

Genetic variation within and between two cultivars of red clover ( Trifolium pratense L.): Comparisons of morphological, isozyme, and RAPD markers  

Microsoft Academic Search

Summary Morphological, isozyme and random amplified polymorphic DNA (RAPD) markers were used to estimate genetic variation within and between cultivars of red clover (Trifolium pratense L.), an important temperate forage legume. Two cultivars of red clover, Essi from Europe and Ottawa from Canada, were evaluated. Six monogenic morphological characters were observed for 80 plants from each of these two cultivars.

P. Kongkiatngam; M. G. Fortin; B. E. Coulman

1995-01-01

306

A population genetic comparison of large- and small-bodied sage grouse in Colorado using microsatellite and mitochondrial DNA markers  

Microsoft Academic Search

Sage grouse ( Centrocercus urophasianus ) from southwestern Colorado and southeastern Utah (United States) are 33% smaller than all other sage grouse and have obvious plumage and behavioural differences. Because of these differences, they have been tentatively recog- nized as a separate 'small-bodied' species. We collected genetic evidence to further test this proposal, using mitochondrial sequence data and microsatellite markers

S. J. Oyler-mccance; N. W. Kahn; K. P. Burnham; C. E. Braun

1999-01-01

307

Genetic variation within and among 22 accessions of three tall larkspur species ( Delphinium spp.) based on RAPD markers  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in three species of toxic larkspurs (Delphinium spp). A total of 184 plants from 22 accessions in five western states were analyzed by 23 RAPD primers that amplified 188 reproducible bands. There were 144 polymorphic bands; 10 shared by Delphinium glaucum and Delphinium occidentale, eight shared by Delphinium

X Li; M. H Ralphs; D. R Gardner; R. R.-C Wang

2002-01-01

308

Genetic characterization of Salix alba L. and Salix fragilis L. by means of different PCR-derived marker systems  

Microsoft Academic Search

Salix alba L. and Salix fragilis L. are two closely related willow species whose phenotypic features, showing a large and continuous variation, have a low diagnostic value for identifying pure species and interspecific hybrids. In this paper, the effectiveness of different multilocus PCR-based molecular markers, such as I-SSRs, RAPDs and AFLPs in detecting genetic polymorphisms able to discriminate the two

S. Meneghetti; G. Barcaccia; P. Paiero; M. Lucchin

2007-01-01

309

ASSESSING GENETIC DIVERSITY AND POPULATION STRUCTURE IN A CITRUS GERMPLASM COLLECTION UTILIZING SIMPLE SEQUENCE REPEAT MARKERS (SSRS)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms among 370 apparently sexually-derived Citrus accessions from the Citrus Variert Collection maintained at the University of California, Riverside. Genetic diversity statistics were calculated for each indivi...

310

Estimation of genetic diversity in some Iranian wild Prunus subgenus Cerasus accessions using inter-simple sequence repeat (ISSR) markers  

Microsoft Academic Search

As Iran is one of the main origins of Prunus germplasm. In this study, ISSR markers were used for genetic diversity evaluation of 39 accessions of subgenus Cerasus belonging to six species i.e. Prunus avium L., Prunus cerasus L., Prunus mahaleb L., Prunus incana Pall., Prunus microcarpa Boiss., and Prunus brachypetala Boiss.. With 12 ISSR primers, 151 polymorphic bands were

Ali Shahi-Gharahlar; Zabihollah Zamani; Reza Fatahi; Naser Bouzari

2011-01-01

311

Evaluation of genetic diversity and relationships within and between two breeds of duck based on microsatellite markers  

Microsoft Academic Search

The genetic diversity of two natural populations (M, N) of Beijing duck (Anas platyrhynchos) and 11 artificially selected lines of Beijing duck (A, B, E–L, O) from China Gold Star Duck Production Ltd., along with two Cherry Valley duck lines (C and D) from the British Cherry Valley Livestock Division, was evaluated using 18 microsatellite markers covering 16 linkage groups.

Fei Wu; Yinghua Huang; Ying Ma; Shengqiang Hu; Jinping Hao; Ning Li

2009-01-01

312

Utilization of RAPD marker to analyze natural genetic variation in Calligonum polygonoides L. - A key stone species of Thar desert  

Microsoft Academic Search

The species Calligonum polygonoides L. of Polygonaceae is one of the most economically important resources of the Indian desert, playing an important role in the lives of local population. A great range of genetic diversity could be seen in diverse populations of this species which are spread all over western Rajasthan. DNA-based molecular markers are playing increasingly important role in

Sangeeta Bewal; Santosh Kumar Sharma; Ajay Parida; Sadha Shivam; Satyawada Rama Rao; Arun Kumar

313

High-density genetic and physical mapping of DNA markers near the X-linked Alport syndrome locus: definition and use of flanking polymorphic markers.  

PubMed

To refine the genetic and physical mapping of the locus for Alport syndrome (ATS), 22 X-chromosome restriction fragment length polymorphism (RFLP) markers that fall between Xq21.3 and Xq25 were tested for genetic linkage with the disease and also mapped with respect to a series of physical breakpoints in this region. The location of the COL4A5 gene, which has recently been shown to be mutated in at least some families with Alport syndrome, was determined with respect to the same physical breakpoints. Two large Utah kindreds were included in the genetic studies, kindreds P and C, with 125 and 63 potentially informative meioses, respectively. Both kindreds have essentially identical nephritis; however, kindred P has sensorineural hearing loss associated with the nephritis, while kindred C does not. A mutation in COL4A5 has been demonstrated for kindred P, but no change in this gene has yet been detected for kindred C. Twelve informative probes did not recombine with the disease locus in either kindred (theta = 0.0, with combined lod scores for the two kindreds ranging from 7.7 to 30.0). The closest markers that could be demonstrated to flank the disease locus were the same for each kindred and thus the locations of the mutations causing the two disease phenotypes are not distinguishable at the current level of genetic resolution. The flanking markers are also useful for the resolution of questionable diagnoses and allow accurate estimates for these families of the rate of sporadic hematuria in noncarrier females (7%) and the penetrance of hematuria for carrier females (93%). PMID:1684566

Barker, D F; Fain, P R; Goldgar, D E; Dietz-Band, J N; Turco, A E; Kashtan, C E; Gregory, M C; Tryggvason, K; Skolnick, M H; Atkin, C L

1991-12-01

314

Novel Tetra-nucleotide Microsatellite DNA Markers for Assessing the Evolutionary Genetics and Demographics of Northern Snakehead (Channa argus) Invading North America  

USGS Publications Warehouse

We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity (averaging 6.8 alleles/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection has not achieved mutation-drift equilibrium. These results were consistent with instances of deviations from Hardy-Weinberg equilibrium and the presence of some linkage disequilibrium. A comparison of individual pair-wise distances suggested the presence of multiple differentiated groups of related individuals. Results of all analyses are consistent with a pattern of multiple, recent introductions. The microsatellite markers developed for C. argus yielded sufficient genetic diversity to potentially: (1) delineate kinship; (2) elucidate fine-scale population structure; (3) define management (eradication) units; (4) estimate dispersal rates; (5) estimate population sizes; and (6) provide unique demographic perspectives of control or eradication effectiveness

King, Timothy L.; Johnson, R.L.

2011-01-01

315

Unique genetic loci identified for emotional behavior in control and chronic stress conditions  

PubMed Central

An individual's genetic background affects their emotional behavior and response to stress. Although studies have been conducted to identify genetic predictors for emotional behavior or stress response, it remains unknown how prior stress history alters the interaction between an individual's genome and their emotional behavior. Therefore, the purpose of this study is to identify chromosomal regions that affect emotional behavior and are sensitive to stress exposure. We utilized the BXD behavioral genetics mouse model to identify chromosomal regions that predict fear learning and emotional behavior following exposure to a control or chronic stress environment. 62 BXD recombinant inbred strains and C57BL/6 and DBA/2 parental strains underwent behavioral testing including a classical fear conditioning paradigm and the elevated plus maze. Distinct quantitative trait loci (QTLs) were identified for emotional learning, anxiety and locomotion in control and chronic stress populations. Candidate genes, including those with already known functions in learning and stress were found to reside within the identified QTLs. Our data suggest that chronic stress history reveals novel genetic predictors of emotional behavior. PMID:25374516

Carhuatanta, Kimberly A. K.; Shea, Chloe J. A.; Herman, James P.; Jankord, Ryan

2014-01-01

316

Shared and Unique Genetic and Environmental Influences on Aging-Related Changes in Multiple Cognitive Abilities  

ERIC Educational Resources Information Center

Aging-related declines occur in many different domains of cognitive function during middle and late adulthood. However, whether a global dimension underlies individual differences in changes in different domains of cognition and whether global genetic influences on cognitive changes exist is less clear. We addressed these issues by applying…

Tucker-Drob, Elliot M.; Reynolds, Chandra A.; Finkel, Deborah; Pedersen, Nancy L.

2014-01-01

317

Developing regional genetic counseling for southern Chinese with nonsyndromic hearing impairment: a unique mutational spectrum  

PubMed Central

Background Racial and regional factors are important for the clinical diagnosis of non-syndromic hearing impairment. Comprehensive genetic analysis of deaf patients in different regions of China must be performed to provide effective genetic counseling. To evaluate the mutational spectrum of south Chinese families, we performed genetic analysis for non-syndromic hearing impairment in this population. Methods Complete clinical evaluations were performed on 701 unrelated patients with non-syndromic hearing impairment from six provinces in south China. Each subject was screened for common mutations, including SLC26A4 c.IVS7-2A?>?G, c.2168A?>?G; mitochondrial DNA m.1555A?>?G, m.1494C?>?T, m.7444G?>?A, m.7445A?>?G; GJB3 c.538C?>?T, c.547G?>?A; and WFS1 c.1901A?>?C, using pyrosequencing. GJB2 and SLC26A4 coding region mutation detection were performed using Sanger sequencing. Results Genetic analysis revealed that among the etiology of non-syndromic hearing impairment, GJB2, SLC26A4, and mitochondrial m.1555A?>?G mutations accounted for 18.0%, 13.1%, and 0.9%, respectively. Common mutations included GJB2 c.235delC, c.109G?>?A, SLC26A4 c.IVS7-2A?>?G, c.1229 T?>?C, and mitochondrial m.1555A?>?G. The total mutation rate was 45.1% in all patients examined in south China. Overall, the clear contribution of GJB2, SLC26A4, and mitochondrial m.1555A?>?G to the etiology of the non-syndromic deafness population in south China was 32.0%. Conclusions Our study is the first genetic analysis of non-syndromic hearing impairment in south China, and revealed that a clear genetic etiology accounted for 32.0% of non-syndromic hearing cases in patients from these regions. The mutational spectrum of non-syndromic hearing impairment in the south Chinese population provides useful and targeted information to aid in genetic counseling. PMID:24612839

2014-01-01

318

Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata.  

PubMed

Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ?900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West-South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe. PMID:23734255

Boattini, Alessio; Martinez-Cruz, Begoña; Sarno, Stefania; Harmant, Christine; Useli, Antonella; Sanz, Paula; Yang-Yao, Daniele; Manry, Jeremy; Ciani, Graziella; Luiselli, Donata; Quintana-Murci, Lluis; Comas, David; Pettener, Davide

2013-01-01

319

Test for interactions between a genetic marker set and environment in generalized linear models  

PubMed Central

We consider in this paper testing for interactions between a genetic marker set and an environmental variable. A common practice in studying gene–environment (GE) interactions is to analyze one single-nucleotide polymorphism (SNP) at a time. It is of significant interest to analyze SNPs in a biologically defined set simultaneously, e.g. gene or pathway. In this paper, we first show that if the main effects of multiple SNPs in a set are associated with a disease/trait, the classical single SNP–GE interaction analysis can be biased. We derive the asymptotic bias and study the conditions under which the classical single SNP–GE interaction analysis is unbiased. We further show that, the simple minimum p-value-based SNP-set GE analysis, can be biased and have an inflated Type 1 error rate. To overcome these difficulties, we propose a computationally efficient and powerful gene–environment set association test (GESAT) in generalized linear models. Our method tests for SNP-set by environment interactions using a variance component test, and estimates the main SNP effects under the null hypothesis using ridge regression. We evaluate the performance of GESAT using simulation studies, and apply GESAT to data from the Harvard lung cancer genetic study to investigate GE interactions between the SNPs in the 15q24–25.1 region and smoking on lung cancer risk. PMID:23462021

Lin, Xinyi; Lee, Seunggeun; Christiani, David C.; Lin, Xihong

2013-01-01

320

Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the Genus Linum  

PubMed Central

SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121

Melnikova, Nataliya V.; Kudryavtseva, Anna V.; Zelenin, Alexander V.; Lakunina, Valentina A.; Yurkevich, Olga Yu.; Speranskaya, Anna S.; Dmitriev, Alexey A.; Krinitsina, Anastasia A.; Belenikin, Maxim S.; Uroshlev, Leonid A.; Snezhkina, Anastasiya V.; Sadritdinova, Asiya F.; Koroban, Nadezda V.; Amosova, Alexandra V.; Samatadze, Tatiana E.; Guzenko, Elena V.; Lemesh, Valentina A.; Savilova, Anastasya M.; Rachinskaia, Olga A.; Kishlyan, Natalya V.; Rozhmina, Tatiana A.; Bolsheva, Nadezhda L.; Muravenko, Olga V.

2014-01-01

321

Genetic differentiation induced by spaceflight treatment of Cistanche deserticola and identification of inter-simple sequence repeat markers associated with its medicinal constituent contents  

NASA Astrophysics Data System (ADS)

The dried, fleshy stems of Cistanche deserticola (Orobanchaceae) are popular tonics in Traditional Chinese Medicine (TCM) to treat the inability of kidney in expelling extra fluid in the body, causing fluid retention, and reform reproductive system. However, the wild plants of C. deserticola have become endangered due to habitat downsizing and over-harvesting for its medicinal usages. The present research was carried out for the following purposes: (1) promoting the space-breeding research; (2) providing molecular evidence for agricultural selective breeding; and (3) protecting this endangered herbal medicine and conserving its genetic resources.In this study, plants were cultivated from seeds specifically treated in spaceflight for seven days, and sampled to screen positive mutants and identify ISSR markers associated with their medicinal constituents. As a result, nine out of the 94 ISSR primers were showed high polymorphism, and a total of 118 bands were generated, of which 80 were polymorphic, ranging from 250 to 2600 bp. The spaceflight mutants were found to have lower coefficient of gene differentiation (Gst = 0.0269), and higher gene flow (Nm = 18.0740) than those of the controls (Gst = 0.2067 and Nm = 1.9185). The results demonstrated that most of the genetic variation were harnessed within populations (>97%). The Analysis of Molecular Variance (AMOVA) revealed high genetic variation within populations (88.03%) and low genetic differentiation among regions (-18.83%) and populations (30.79%), respectively. The results also indicated a profound difference between spaceflight condition and that on the earth. The unique vacuum environment of spaceflight was suggested to induce DNA mutation and various variations of C. deserticola. In addition, six particular ISSR markers were identified, cloned and sequenced; one of them, CA41939-934, was found positively correlated with acteoside with correlation coefficient values of 0.264 (P < 0.05). Our work may provide a valuable molecular evidence for establishing conservation strategies and space-breeding research program.

Wu, Y.; Yang, D. Y.; Tu, P. F.; Tian, Y. Z.; Guo, Y. H.; Wang, X. M.; Li, X. B.

2011-02-01

322

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species  

PubMed Central

Background and Aims Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne ‘Cashel’. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Methods Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. Key Results All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A8 mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. Conclusions The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species. PMID:22419761

Diekmann, Kerstin; Hodkinson, Trevor R.; Barth, Susanne

2012-01-01

323

Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems.  

PubMed

Potato (Solanum tuberosum) is an important non-cereal crop throughout the world and is highly recommended for ensuring global food security. Owing to the complexities in genetics and inheritance pattern of potato, the conventional method of cross breeding for developing improved varieties has been difficult. Identification and tagging of desirable traits with informative molecular markers would aid in the development of improved varieties. Insertional polymorphism of copia-like and gypsy-like long terminal repeat retrotransposons (RTN) were investigated among 47 potato varieties from India using Inter-Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) marker techniques and were compared with the DNA profiles obtained with simple sequence repeats (SSRs). The genetic polymorphism, efficiency of polymorphism and effectiveness of marker systems were evaluated to assess the extent of genetic diversity among Indian potato varieties. A total of 139 polymorphic SSR alleles, 270 IRAP and 98 REMAP polymorphic bands, showing polymorphism of 100%, 87.9% and 68.5%, respectively, were used for detailed characterization of the genetic relationships among potato varieties by using cluster analysis and principal coordinate analysis (PCoA). IRAP analysis resulted in the highest number of polymorphic bands with an average of 15 polymorphic bands per assay unit when compared to the other two marker systems. Based on pair-wise comparison, the genetic similarity was calculated using Dice similarity coefficient. The SSRs showed a wide range in genetic similarity values (0.485-0.971) as compared to IRAP (0.69-0.911) and REMAP (0.713-0.947). A Mantel's matrix correspondence test showed a high positive correlation (r=0.6) between IRAP and REMAP, an intermediate value (r=0.58) for IRAP and SSR and the lowest value (r=0.17) for SSR and REMAP. Statistically significant cophenetic correlation coefficient values, of 0.961, 0.941 and 0.905 were observed for REMAP, IRAP and SSR, respectively. The widespread presence and distinct DNA profiles for copia-like and gypsy-like RTNs in the examined genotypes indicate that these elements are active in the genome and may have even contributed to the potato genome organization. Although the three marker systems were capable of distinguishing all the 47 varieties; high reproducibility, low cost and ease of DNA profiling data collection make IRAP and REMAP markers highly efficient whole-genome scanning molecular probes for population genetic studies. Information obtained from the present study regarding the genetic association and distinctiveness provides an useful guide for selection of germplasm for plant breeding and conservation efforts. PMID:24440815

Sharma, Vishakha; Nandineni, Madhusudan R

2014-04-01

324

Genetic Differentiation and Efficient Sex-specific Marker Development of a Pair of Y- and X-linked Markers in Yellow Catfish  

PubMed Central

Pf62-Y and Pf62-X is a pair of allelic Y chromosome-linked and X chromosome-linked markers, and have been used to identify YY super-males, XY males and XX females for commercial production of all-male populations in yellow catfish (Pelteobagrus fulvidraco). However, the SCAR primers used previously have only two nucleotide difference, which restricts the wide utility because of nucleotide polymorphism. In this study, a continuous 8102 bp Pf62-Y sequence and a 5362 bp Pf62-X sequence have been cloned by genome walking, and significant genetic differentiation has been revealed between the corresponding X and Y chromosome allele sequences. Moreover, three pairs of primers were designed to efficiently identify YY super-males, XY males and XX females in an artificial breeding population, and to distinguish XY males and XX females in various wild populations. Together, the three new sex-specific genetic markers develop a highly stable and efficient method for genetic sex identification and sex control application in sustainable aquaculture of all-male yellow catfish. PMID:24250249

Dan, Cheng; Mei, Jie; Wang, Da; Gui, Jian-Fang

2013-01-01

325

Animal models of physiologic markers of male reproduction: genetically defined infertile mice  

SciTech Connect

The present report focuses on novel animal models of male infertility: genetically defined mice bearing single-gene mutations that induce infertility. The primary goal of the investigations was to identify the reproductive defects in these mutant mice. The phenotypic effects of the gene mutations were deciphered by comparing the mutant mice to their normal siblings. Initially testicular steroidogenesis and spermatogenesis were investigated. The physiologic markers for testicular steroidogenesis were steroid secretion by testes perifused in vitro, seminal vesicle weight, and Leydig cell histology. Spermatogenesis was evaluated by the enumeration of homogenization-resistant sperm/spermatids in testes and by morphometric analyses of germ cells in the seminiferous epithelium. If testicular function appeared normal, the authors investigated the sexual behavior of the mice. The parameters of male sexual behavior that were quantified included mount patency, mount frequency, intromission latency, thrusts per intromission, ejaculation latency, and ejaculation duration. Females of pairs breeding under normal circumstances were monitored for the presence of vaginal plugs and pregnancies. The patency of the ejaculatory process was determined by quantifying sperm in the female reproductive tract after sexual behavior tests. Sperm function was studied by quantitatively determining sperm motility during videomicroscopic observation. Also, the ability of epididymal sperm to function within the uterine environment was analyzed by determining sperm capacity to initiate pregnancy after artificial insemination. Together, the experimental results permitted the grouping of the gene mutations into three general categories. They propose that the same biological markers used in the reported studies can be implemented in the assessment of the impact that environmental toxins may have on male reproduction.

Chubb, C.

1987-10-01

326

Genetic Rearrangements of Six Wheat–Agropyron cristatum 6P Addition Lines Revealed by Molecular Markers  

PubMed Central

Agropyron cristatum (L.) Gaertn. (2n?=?4x?=?28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat–A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat–A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330

Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

2014-01-01

327

Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers.  

PubMed

Agropyron cristatum (L.) Gaertn. (2n?=?4x?=?28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat-A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat-A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330

Han, Haiming; Bai, Li; Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

2014-01-01

328

Age-Related Shifts in the Density and Distribution of Genetic Marker Water Quality Indicators in Cow and Calf Feces  

PubMed Central

Calves make up about 16% of the current bovine population in the United States and can excrete high levels of human pathogens in their feces. We describe the density and distribution of genetic markers from 9 PCR- and real-time quantitative PCR-based assays, including CF128, CF193, CowM2, CowM3, GenBac3, Entero1, EC23S857, CampF2, and ttr-6, commonly used to help assess ambient surface water quality. Each assay was tested against a collection of 381 individual bovine fecal samples representing 31 mother and calf pairings collected over a 10-month time period from time of birth through weaning. Genetic markers reported to be associated with ruminant and/or bovine fecal pollution were virtually undetected in calves for up to 115 days from birth, suggesting that physiological changes in calf ruminant function impact host-associated genetic marker shedding. In addition, general fecal indicator markers for Bacteroidales, Escherichia coli, and Enterococcus spp. exhibited three separate trends across time, indicating that these bacteria respond differently to age-related physiological and dietary changes during calf development. The results of this study suggest that currently available PCR-based water quality indicator technologies can under- or overestimate fecal pollution originating from calves and identify a need for novel calf-associated source identification methods. PMID:24362434

Kelty, Catherine A.; Peed, Lindsay; Sivaganesan, Mano; Mooney, Thomas; Jenkins, Michael

2014-01-01

329

Applicability of universal Bacteroidales genetic marker for microbial monitoring of drinking water sources in comparison to conventional indicators.  

PubMed

Water quality monitoring is essential for the provision of safe drinking water. In this study, we compared a selection of fecal indicators with universal Bacteroidales genetic marker to identify fecal pollution of a variety of drinking water sources. A total of 60 samples were collected from water sources. The microbiological parameters included total coliforms, fecal coliforms, Escherichia coli and fecal streptococci as the fecal indicator bacteria (FIB), Clostridium perfringens and H2S bacteria as alternative indicators, universal Bacteroidales genetic marker as a promising alternative fecal indicator, and Salmonella spp., Shigella spp., and E. coli O157 as pathogenic bacteria. From 60 samples analyzed, Bacteroidales was the most frequently detected indicator followed by total coliforms. However, the Bacteroidales assay failed to detect the marker in nine samples positive for FIB and other alternative indicators. The results of our study showed that the absence of Bacteroidales is not necessarily an evidence of fecal and pathogenic bacteria absence and may be unable to ensure the safety of the water. Further research, however, is required for a better understanding of the use of a Bacteroidales genetic marker as an indicator in water quality monitoring programs. PMID:25023746

Shahryari, A; Nikaeen, M; Khiadani Hajian, M; Nabavi, F; Hatamzadeh, M; Hassanzadeh, A

2014-11-01

330

SIRP? and FHOD1 are unique markers of littoral cells, a recently evolved major cell population of red pulp of human spleen  

PubMed Central

Asplenic individuals are compromised not only in their ability to destroy infectious agents, but are at increased risk of death from autoimmune disease, certain tumors, and ischemic heart disease. Enhanced mortality is attributed to lack of phagocytes sequestered in spleen that efficiently engulf and destroy appropriate targets, though related cells are found elsewhere. To determine whether a unique population regulates RBC-pathogen clearance and filtration of altered self, we reviewed the anatomic literature and analyzed in situ by immunohistochemistry and immunofluorescence the expression patterns of a little-characterized cell that dominates the splenic red pulp of man and closely related primates-the venous sinus lining or littoral cell (LC). High expression of the formin FHOD1 outlines the LC population. Though LCs are endothelial-like in distribution they express several macrophage directed proteins, the RBC antigen DARC and T-cell co-receptor CD8?/? yet they lack lineage-associated markers CD34 and CD45. Strikingly, SIRP? (CD172a) expression in human spleen concentrates on LCs, consistent with recent demonstration of a key role in RBC turnover and elimination versus release of infected or altered self. Our results indicate human LCs (SIRP?+, FHOD1+, CD8?/?+, CD34?, CD45?) comprise a highly plastic barrier cell population that emerged late in primate evolution coordinate with CD8 expression. Unique to Hominidae, LCs may be the ultimate determinant of which cells re-circulate after passage through human spleen. PMID:22490440

Ogembo, Javier Gordon; Milner, Danny A.; Mansfield, Keith G.; Rodig, Scott J.; Murphy, George F.; Kutok, Jeffery L.; Pinkus, Geraldine S.; Fingeroth, Joyce D.

2012-01-01

331

Genetic variants and environmental factors associated with hormonal markers of ovarian reserve in Caucasian and African American women  

PubMed Central

BACKGROUND The ovarian reserve (number and quality of oocytes) is correlated with reproductive potential as well as somatic health, and is likely to have multiple genetic and environmental determinants. Several reproductive hormones are closely linked with the oocyte pool and thus can serve as surrogate markers of ovarian reserve. However, we know little about the underlying genes or genetic variants. METHODS We analyzed genetic variants across the genome associated with two hormonal markers of ovarian reserve, FSH and anti-Mullerian hormone, in a reproductively normal population of Caucasian (n = 232) and African American (n = 200) women, aged 25–45 years. We also examined the effects of environmental or lifestyle factors on ovarian reserve phenotypes. RESULTS We identified one variant approaching genome-wide significance (rs6543833; P= 8.07 × 10?8) and several nominal variants nearby and within the myeloid-associated differentiation marker-like (MYADML) gene, that were associated with FSH levels in African American women; these were validated in Caucasian women. We also discovered effects of smoking and oral contraceptive use on ovarian reserve phenotypes, with alterations in several reproductive hormones. CONCLUSIONS This work is the largest study on ovarian reserve in women of reproductive age and is the only genome-wide study on ovarian reserve markers. The genes containing or near the identified variants have no known roles in ovarian biology and represent interesting candidate genes for future investigations. The discovery of genetic markers may lead to better long-range predictions of declining ovarian function, with implications for reproductive and somatic health. PMID:22116950

Schuh-Huerta, Sonya M.; Johnson, Nicholas A.; Rosen, Mitchell P.; Sternfeld, Barbara; Cedars, Marcelle I.; Reijo Pera, Renee A.

2012-01-01

332

Use of a genetically-engineered Escherichia coli strain as a sample process control for quantification of the host-specific bacterial genetic markers.  

PubMed

Quantitative PCR (qPCR) assays targeting the host-specific Bacteroides-Prevotella 16S rRNA genetic markers have been proposed as one of the promising approaches to identify the source of fecal contamination in environmental waters. One of the concerns of qPCR assays to environmental samples is the reliability of quantified values, since DNA extraction followed by qPCR assays are usually performed without appropriate sample process control (SPC) and internal amplification controls (IACs). To check the errors in sample processing and improve the reliability of qPCR results, it is essential to evaluate the DNA recovery efficiency and PCR amplification efficiency of the target genetic markers and correct the measurement results. In this study, we constructed a genetically-engineered Escherichia coli K12 strain (designated as strain MG1655 ?lac::kan) as sample process control and evaluated the applicability to environmental water samples. The recovery efficiency of the SPC strain MG1655 ?lac::kan was similar to that of Bacteroides fragilis JCM 11019, when DNA were extracted from water samples spiked with the two bacteria. Furthermore, the SPC was included in the qPCR assays with propidium monoazide (PMA) treatment, which can exclude the genetic markers from dead cells. No significant DNA loss was observed in the PMA treatment. The inclusion of both the SPC (strain MG1655 ?lac::kan) and IAC in qPCR assays with PMA treatment gave the assurance of reliable results of host-specific Bacteroides-Prevotella 16S rRNA genetic markers in environmental water samples. PMID:23989919

Kobayashi, Ayano; Sano, Daisuke; Taniuchi, Asami; Ishii, Satoshi; Okabe, Satoshi

2013-10-01

333

Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker.  

Technology Transfer Automated Retrieval System (TEKTRAN)

Knowledge of genetic diversity, particularly in an introduced crop species, is crucial to the management and utilization of the genetic resources available. Using capillary electrophoresis system, microsatellite markers were used to determine genetic diversity in 574 accessions of cacao, Theobroma c...

334

Measuring the genetic diversity of Arabian Oryx using microsatellite markers: implication for captive breeding.  

PubMed

Arabian oryx (Oryx leucoryx) is an endangered antelope that is being protected by captive breeding programs. However, the long term success of these programs mainly depends on the prudent use of molecular information for conservation management. We have used an array of seven microsatellite loci to examine the molecular diversity in a representative population of 24 captive-bred and reintroduced Arabian oryx. The locus-wise mean observed heterozygosity (0.601) was found to be comparatively higher than the mean expected heterozygosity (0.565). The specimen-wise observed heterozygosity ranged from 0.143 to 1.00 with an average of 0.60 whereas the mean d(2) varied from 0.57 to 1023.428 with an average value of 223.357. The results of Shannon information index (I = 0.898) also indicated a high level of within population genetic diversity. The average gene flow was 0.298, ranging between 0.204 and 0.424 for different loci. In conclusion, the information about the extent of heterozygosity, allelic diversity and inbreeding/outbreeding depression using microsatellite markers could be of potential relevance for the management of captive breeding programs for the conservation of Arabian oryx. PMID:20558900

Arif, Ibrahim A; Khan, Haseeb A; Shobrak, Mohammad; Homaidan, Ali A Al; Sadoon, Mohammad Al; Farhan, Ahmad H Al

2010-04-01

335

Assessing the genetic relationships of Curcuma alismatifolia varieties using simple sequence repeat markers.  

PubMed

The genus Curcuma is a member of the ginger family (Zingiberaceae) that has recently become popular for use as flowering pot plants, both indoors and as patio and landscape plants. We used PCR-based molecular markers (SSRs) to elucidate genetic variation and relationships between five varieties of Curcuma (Curcuma alismatifolia) cultivated in Malaysia. Of the primers tested, 8 (of 17) SSR primers were selected for their reproducibility and high rates of polymorphism. The number of presumed alleles revealed by the SSR analysis ranged from two to six alleles, with a mean value of 3.25 alleles per locus. The values of HO and HE ranged from 0 to 0.8 (mean value of 0.2) and 0.1837 to 0.7755 (mean value of 0.5102), respectively. Eight SSR primers yielded 26 total amplified fragments and revealed high rates of polymorphism among the varieties studied. The polymorphic information content varied from 0.26 to 0.73. Dice's similarity coefficient was calculated for all pairwise comparisons and used to construct an unweighted pair group method with arithmetic average (UPGMA) dendrogram. Similarity coefficient values from 0.2105 to 0.6667 (with an average of 0.4386) were found among the five varieties examined. A cluster analysis of data using a UPGMA algorithm divided the five varieties/hybrids into 2 groups. PMID:25222232

Taheri, S; Abdullah, T L; Abdullah, N A P; Ahmad, Z; Karimi, E; Shabanimofrad, M R

2014-01-01

336

Expression of inflammatory markers in a genetic rodent model of depression.  

PubMed

The complex bidirectional communication between the central nervous system and the peripheral immune system is of possible relevance for both normal brain functions and the development of psychiatric disorders. The aim of this investigation was to study central expression of inflammatory markers in a genetic rat model of depression (the Flinders sensitive line (FSL) and its control, the Flinders resistant line (FRL)). A peripheral immune activation was induced by lipopolysaccharide (LPS) in order to investigate possible differences in immune reactions between the two rat lines. To confirm behavioural differences between the rat lines the forced swim test was performed, a test to assess depressive-like behaviour. Expression of candidate inflammatory genes was measured in amygdala, hippocampus, hypothalamus, prefrontal cortex and striatum using quantitative real time PCR. Our results show, for the first time, significantly lower central expression of the glial-specific protein S100B and complement factor C3 in several brain regions of the FSL rats compared to controls, both at baseline and after peripheral immune stimulation. No significant differences in immune responses to LPS were observed between the rats lines. Both S100B and C3 have been suggested to be of relevance for brain development and plasticity as well as brain disorders. These proteins may be of importance for the behavioural differences between the FSL and FRL rats, and this model may be useful in studies exploring the influence of the immune system on brain functions. PMID:25277840

Strenn, Nina; Suchankova, Petra; Nilsson, Staffan; Fischer, Christina; Wegener, Gregers; Mathé, Aleksander A; Ekman, Agneta

2015-03-15

337

Spectroscopic detection of fluorescent protein marker gene activity in genetically modified plants  

NASA Astrophysics Data System (ADS)

This work focuses on developing a portable fibre optic fluorescence analyser for rapid identification of genetically modified plants tagged with a fluorescent marker gene. Independent transgenic tobacco plant lines expressing the enhanced green fluorescence protein (EGFP) gene were regenerated following Agrobacterium-mediated gene transfer. Molecular characterisation of these plant lines was carried out at the DNA level by PCR screening to confirm their transgenic status. Conventional transgene expression analysis was then carried out at the RNA level by RT-PCR and at the protein level by Western blotting using anti-GFP rabbit antiserum. The amount of plant-expressed EGFP on a Western blot was quantified against known amounts of purified EGFP by scanning densitometry. The expression level of EGFP in transformed plants was found to range from 0.1 - 0.6% of total extractable protein. A comparison between conventional western analysis of transformants and direct spectroscopic quantification using the fibre optic fluorescence analyser was made. The results showed that spectroscopic measurements of fluorescence emission from strong EGFP expressors correlated positively with Western blot data. However, the fluorescence analyser was also able to identify weakly expressing plant transformants below the detection limit of colorimetric Western blotting.

Liew, O. W.; Chong, Jenny P. C.; Asundi, Anand K.

2005-04-01

338

Identification of genetic risk associated with prostate cancer using ancestry informative markers  

PubMed Central

BACKGROUND Prostate cancer (PCa) is a common malignancy and a leading cause of cancer death among men in the United States with African-American (AA) men having the highest incidence and mortality rates. Given recent results from admixture mapping and genome-wide association studies for PCa in AA men, it is clear that many risk alleles are enriched in men with West African genetic ancestry. METHODS A total of 77 ancestry informative markers (AIMs) within surrounding candidate gene regions were genotyped and haplotyped using Pyrosequencing in 358 unrelated men enrolled in a PCa genetic association study at the Howard University Hospital between 2000 and 2004. Sequence analysis of promoter region single-nucleotide polymorphisms (SNPs) to evaluate disruption of transcription factor-binding sites was conducted using in silico methods. RESULTS Eight AIMs were significantly associated with PCa risk after adjusting for age and West African ancestry. SNP rs1993973 (intervening sequences) had the strongest association with PCa using the log-additive genetic model (P = 0.002). SNPs rs1561131 (genotypic, P = 0.007), rs1963562 (dominant, P = 0.01) and rs615382 (recessive, P = 0.009) remained highly significant after adjusting for both age and ancestry. We also tested the independent effect of each significantly associated SNP and rs1561131 (P = 0.04) and rs1963562 (P = 0.04) remained significantly associated with PCa development. After multiple comparisons testing using the false discovery rate, rs1993973 remained significant. Analysis of the rs156113–, rs1963562–rs615382l and rs1993973–rs585224 haplotypes revealed that the least frequently found haplotypes in this population were significantly associated with a decreased risk of PCa (P = 0.032 and 0.0017, respectively). CONCLUSIONS The approach for SNP selection utilized herein showed that AIMs may not only leverage increased linkage disequilibrium in populations to identify risk and protective alleles, but may also be informative in dissecting the biology of PCa and other health disparities. PMID:22801071

Ricks-Santi, LJ; Apprey, V; Mason, T; Wilson, B; Abbas, M; Hernandez, W; Hooker, S; Doura, M; Bonney, G; Dunston, G; Kittles, R; Ahaghotu, C

2014-01-01

339

Genetic variation and clonal diversity of Bromus ircutensis Kom. in the Otingdag sandy land detected by ISSR markers.  

PubMed

Genetic variation and clonal diversity of nine populations of Bromus ircutensis Kom. from the Otingdag sandy land were investigated using Inter Simple Sequence Repeat (ISSR) markers. A total of 102 bands were amplified by using II ISSR primers chosen for the study. Among those 99% were polymorphic indicating high level of genetic variation at the species level with a mean genetic diversity (H) of 0.292 and Shannon information index (1) of 0.450. Percentage of polymorphic loci (PPL) of nine populations was 76.48% on average, which provides more evidence of considerable genetic variation at the population level. AMOVA analysis revealed that total genetic variation was higher within populations (87.06%) than between populations (12.94%), which is mainly the result of the extensive gene flow (Nm = 1.682) among B. ircutensis populations. UPGMA cluster analysis divided the nine populations into two groups. There was significant or moderate negative correlations between genetic diversity parameters (PPL, H, 1) and longitude or latitude. Mantel test also showed a significant correlation between geographical distance and genetic distance (r = 0.681, p = 0.002). Our findings indicated that distribution of B. ircutensis populations was influenced by geographical and ecological factors. Clonal diversity was also high with 108 individuals identified by 11 ISSR primers being all of different genets. Our results provide a molecular basis for sustainable management and conservation ofB. ircutensis in the study area. PMID:21866860

Yu, T; Han, B; Tian, Q; Liu, A

2011-06-01

340

Evaluating a unique, specialist psychiatric genetic counseling clinic: uptake and impact.  

PubMed

People with psychiatric disorders and their family members have expressed interest in receiving genetic counseling (GC). In February 2012, we opened the first (to our knowledge) specialist psychiatric GC clinic of its kind, for individuals with non-syndromic psychiatric disorders and their families. Prior to GC and at a standard 1-month follow-up session, clinical assessment tools are completed, specifically, the GC outcomes scale (GCOS, which measures empowerment, completed by all clients) and the Illness Management Self Efficacy scale (IMSES, completed by those with mental illness). Consecutive English-speaking clients attending the clinic between 1 February 2012 and 31 January 2013 who were capable of consenting were asked for permission to use their de-identified clinical data for research purposes. Descriptive analyses were conducted to ascertain demographic details of attendees, and paired sample t-tests were conducted to assess changes in GCOS and IMSES scores from pre- to post-GC. Of 143 clients, seven were unable to consent, and 75/136 (55.1%) consented. Most were female (85.3%), self-referred (76%), and had personal experience of mental illness (65.3%). Mean GCOS and IMSES scores increased significantly after GC (p?

Inglis, A; Koehn, D; McGillivray, B; Stewart, S E; Austin, J

2015-03-01

341

New microsatellite markers for examining genetic variation in peripheral and core populations of the Coastal Giant Salamander (Dicamptodon tenebrosus).  

PubMed

The Coastal Giant Salamander (Dicamptodon tenebrosus) is classified as threatened at the northern periphery of its range in British Columbia (BC), Canada, primarily due to forestry practices and habitat fragmentation. Characterising dispersal behaviour and population connectivity is therefore a priority for this region, while genetic differentiation in core versus peripheral locations remains unstudied in this wide-ranging species. We present seven new polymorphic microsatellite markers for use in population genetic analyses of D. tenebrosus. We examine locus characteristics and genetic variation in 12 streams at the species' northern range limit in BC, and within two regions representing sub-peripheral (North Cascades) and core localities (South Cascades) in Washington State, United States. In BC, the number of alleles per locus ranged from 2-5 and observed heterozygosity ranged from 0.044-0.825. Genetic differentiation was highest between BC and the South Cascades, and intermediate between BC and the North Cascades. Across loci, mean allelic richness was similar across regions, while private allelic richness was highest in the core locality (corrected for sample size). These new microsatellite loci will be a valuable addition to existing markers for detailed landscape and population genetic analyses of D. tenebrosus across its range. PMID:21179519

Dudaniec, Rachael Y; Storfer, Andrew; Spear, Stephen F; Richardson, John S

2010-01-01

342

Development of Cymbidium ensifolium genic-SSR markers and their utility in genetic diversity and population structure analysis in cymbidiums.  

PubMed

Background Cymbidium is a genus of 68 species in the orchid family, with extremely high ornamental value. Marker-assisted selection has proven to be an effective strategy in accelerating plant breeding for many plant species. Analysis of cymbidiums genetic background by molecular markers can be of great value in assisting parental selection and breeding strategy design, however, in plants such as cymbidiums limited genomic resources exist. In order to obtain efficient markers, we deep sequenced the C. ensifolium transcriptome to identify simple sequence repeats derived from gene regions (genic-SSR).ResultThe 7,936 genic-SSR markers were identified. A total of 80 genic-SSRs were selected, and primers were designed according to their flanking sequences. Of the 80 genic-SSR primer sets, 62 were amplified in C. ensifolium successfully, and 55 showed polymorphism when cross-tested among 9 Cymbidium species comprising 59 accessions. Unigenes containing the 62 genic-SSRs were searched against Non-redundant (Nr), Gene Ontology database (GO), eukaryotic orthologous groups (KOGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The search resulted in 53 matching Nr sequences, of which 39 had GO terms, 18 were assigned to KOGs, and 15 were annotated with KEGG. Genetic diversity and population structure were analyzed based on 55 polymorphic genic-SSR data among 59 accessions. The genetic distance averaged 0.3911, ranging from 0.016 to 0.618. The polymorphic index content (PIC) of 55 polymorphic markers averaged 0.407, ranging from 0.033 to 0.863. A model-based clustering analysis revealed that five genetic groups existed in the collection. Accessions from the same species were typically grouped together; however, C. goeringii accessions did not always form a separate cluster, suggesting that C. goeringii accessions were polyphyletic.ConclusionThe genic-SSR identified in this study constitute a set of markers that can be applied across multiple Cymbidium species and used for the evaluation of genetic relationships as well as qualitative and quantitative trait mapping studies. Genic-SSR¿s coupled with the functional annotations provided by the unigenes will aid in mapping candidate genes of specific function. PMID:25481640

Li, Xiaobai; Jin, Feng; Jin, Liang; Jackson, Aaron; Huang, Cheng; Li, Kehu; Shu, Xiaoli

2014-12-01

343

Combination of Genetic and Quantitative Serological Immune Markers are Associated with Complicated Crohn’s Disease Behavior  

PubMed Central

Background Treatment of Crohn’s disease (CD) with biologics may alter disease progression, leading to fewer disease-related complications, but cost and adverse event profiles often limit their effective use. Tools identifying patients at high risk of complications, who would benefit the most from biologics, would be valuable. Previous studies suggest that biomarkers may aid in determining the course of CD. We aimed to determine if combined serologic immune responses and NOD2 genetic markers are associated with CD complications. Methods In this cross-sectional study, banked blood from well-characterized CD patients (n = 593; mean follow-up: 12 years) from tertiary and community centers was analyzed for six serological biomarkers (ASCA-IgA, ASCA-IgG, anti-OmpC, anti-CBir1, anti-I2, pANCA). In a patient subset (n = 385), NOD2 (SNP8, SNP12, SNP13) genotyping was performed. Complications included stricturing and penetrating disease behaviors. A logistic regression model for the risk of complications over time was constructed and evaluated by cross-validation. Results For each serologic marker, complication rates were stratified by quartile. Complication frequency was significantly different across quartiles for each marker (P trend ? 0.001). Patients with SNP13 NOD2 risk alleles experienced increased complications versus patients without NOD2 mutations (P ? 0.001). A calibration plot of modeled versus observed complication rates demonstrated good agreement (R = 0.973). Performance of the model integrating serologic and genetic markers was demonstrated by area under the receiver operating characteristic curve (AUC = 0.801; 95% confidence interval: 0.757–0.846). Conclusions This model combining serologic and NOD2 genetic markers may provide physicians with a tool to assess the probability of patients developing a complication over the course of CD. PMID:21391291

Lichtenstein, Gary R.; Targan, Stephan R.; Dubinsky, Marla C.; Rotter, Jerome I.; Barken, Derren M.; Princen, Fred; Carroll, Susan; Brown, Michelle; Stachelski, Jordan; Chuang, Emil; Landers, Carol J.; Stempak, Joanne M.; Singh, Sharat; Silverberg, Mark S.

2014-01-01

344

Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers  

PubMed Central

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r2 decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod. PMID:22428056

Bouchet, Sophie; Pot, David; Deu, Monique; Rami, Jean-François; Billot, Claire; Perrier, Xavier; Rivallan, Ronan; Gardes, Laëtitia; Xia, Ling; Wenzl, Peter; Kilian, Andrzej; Glaszmann, Jean-Christophe

2012-01-01

345

Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers--is it feasible?  

PubMed

Fecal pollution is measured in surface waters using culture-based measurements of enterococci and Escherichia coli bacteria. Source apportionment of these two fecal indicator bacteria is an urgent need for prioritizing remediation efforts and quantifying health risks associated with source-specific pathogens. There are a number of quantitative real-time PCR (QPCR) assays that estimate concentrations of source-associated genetic markers; however, their concentrations are not necessarily amenable to source apportionment because the markers may differ in prevalence across sources. Here we mathematically derive and test, under ideal conditions, a method that utilizes the ratios of fecal source-associated genetic markers and culture and molecular measurements of general fecal indicators to apportion enterococci and E. coli. The source contribution is approximately equal to the ratio of the source-associated and the general fecal indicator concentrations in a water sample divided by their ratio in the source material, so long as cross-reactivity is negligible. We illustrate the utility of the ratio method using samples consisting of mixtures of various fecal pollution sources. The results from the ratio method correlated well with the actual source apportionment in artificial samples. However, aging of contamination can confound source allocation predictions. In particular, culturable enterococci and E. coli, the organisms presently regulated in the United States and much of the world, decay at different rates compared to source-associated markers and as a result cannot be apportioned using this method. However, limited data suggest a similar decay rate between source-associated and QPCR-measured Enterococcus and E. coli genetic markers, indicating that apportionment may be possible for these organisms; however further work is needed to confirm. PMID:23890872

Wang, Dan; Farnleitner, Andreas H; Field, Katharine G; Green, Hyatt C; Shanks, Orin C; Boehm, Alexandria B

2013-11-15

346

GENETIC ANALYSIS OF FAMILIES WITH AUTOIMMUNE DIABETES AND THYROIDITIS: EVIDENCE FOR COMMON AND UNIQUE GENES  

PubMed Central

Context: Epidemiological data suggest a common genetic susceptibility to Type 1 diabetes (T1D) and autoimmune thyroid disease (AITD). Objective: Our objective was to identify the joint susceptibility genes for T1D and AITD. Design: We conducted a family based linkage and association study. Setting: The study took place at an academic medical center. Participants: Participants included 55 multiplex families (290 individuals) in which T1D and AITD clustered (T1D-AITD families). Main Outcome Measures: We conducted tests for linkage and family-based associations (transmission disequilibrium test) with four candidate genes, human leukocyte antigen (HLA), cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), insulin variable number of tandem repeats (VNTR), and thyroglobulin. Results: Linkage evidence to HLA appeared when subjects with either T1D or AITD were considered affected [maximum LOD score (MLS), 2.2]. The major HLA haplotype contributing to the shared susceptibility was DR3-DQB1*0201, with DR3 conferring most of the shared risk. The CTLA-4 gene showed evidence for linkage only when individuals with both T1D and AITD were considered affected (MLS, 1.7), and the insulin VNTR showed evidence for linkage when individuals with either T1D or AITD were considered affected (MLS, 1.9); i.e. it may contribute to the familial aggregation of T1D and AITD. Conclusions: The HLA class II locus contributes to the shared risk for T1D and AITD, and the major HLA haplotype contributing to this association is DR3-DQB1*0201. Additional non-HLA loci contribute to the joint susceptibility to T1D and AITD, and two potential candidates include the CTLA-4 and insulin VNTR loci. PMID:15928253

Golden, Brian; Levin, Lara; Ban, Yoshiyuki; Concepcion, Erlinda; Greenberg, David A.

2005-01-01

347

RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat.  

PubMed

The identification of genetic markers linked to genes of agronomic importance is a major aim of crop research and breeding programmes. Here, we identify markers for Yr15, a major disease resistance gene for wheat yellow rust, using a segregating F2 population. After phenotyping, we implemented RNA sequencing (RNA-Seq) of bulked pools to identify single-nucleotide polymorphisms (SNP) associated with Yr15. Over 27 000 genes with SNPs were identified between the parents, and then classified based on the results from the sequenced bulks. We calculated the bulk frequency ratio (BFR) of SNPs between resistant and susceptible bulks, selecting those showing sixfold enrichment/depletion in the corresponding bulks (BFR > 6). Using additional filtering criteria, we reduced the number of genes with a putative SNP to 175. The 35 SNPs with the highest BFR values were converted into genome-specific KASP assays using an automated bioinformatics pipeline (PolyMarker) which circumvents the limitations associated with the polyploid wheat genome. Twenty-eight assays were polymorphic of which 22 (63%) mapped in the same linkage group as Yr15. Using these markers, we mapped Yr15 to a 0.77-cM interval. The three most closely linked SNPs were tested across varieties and breeding lines representing UK elite germplasm. Two flanking markers were diagnostic in over 99% of lines tested, thus providing a reliable haplotype for marker-assisted selection in these breeding programmes. Our results demonstrate that the proposed methodology can be applied in polyploid F2 populations to generate high-resolution genetic maps across target intervals. PMID:25382230

Ramirez-Gonzalez, Ricardo H; Segovia, Vanesa; Bird, Nicholas; Fenwick, Paul; Holdgate, Sarah; Berry, Simon; Jack, Peter; Caccamo, Mario; Uauy, Cristobal

2014-11-01

348

A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP®, RFLP and SSR markers  

Microsoft Academic Search

Using AFLP technology and a recombinant inbred line population derived from the sorghum cross of BTx623 × IS3620C, a high-density genetic map of the sorghum genome was constructed. The 1713 cM map encompassed 2926 loci distributed on ten linkage groups; 2454 of those loci are AFLP products generated from either the EcoRI\\/MseI or PstI\\/MseI enzyme combinations. Among the non-AFLP markers, 136

M. A. Menz; R. R. Klein; J. E. Mullet; J. A. Obert; N. C. Unruh; P. E. Klein

2002-01-01

349

Genetic structure in fragmented populations of Hippophae rhamnoides ssp. sinensis in China investigated by ISSR and cpSSR markers  

Microsoft Academic Search

Hippophae\\u000a rhamnoides ssp. sinensis is an ecologically and economically important species that has been widely used as a pioneer plant in China. In this study,\\u000a we employed both nuclear ISSR and maternal cpSSR markers to survey the genetic diversity and structure of populations of ssp.\\u000a sinensis representing three different landscapes, the northwestern desert and grassland region, the alpine vegetation region

Yuhua WangHao; Hao Jiang; Shuming Peng; Helena Korpelainen

2011-01-01

350

Identification and genetic diversity analysis of date palm (Phoenix dactylifera L.) varieties from Morocco using RAPD markers  

Microsoft Academic Search

Genetic variation among 43 date palm (Phoenix dactylifera L.) accessions, including 37 accessions from Morocco and 6 cultivars\\u000a from Iraq and Tunisia, was studied using Random Amplified Polymorphic DNA (RAPD) markers. The pre-screening of 123 primers\\u000a on four genotypes allowed selection of 19 primers which revealed polymorphism and gave reproducible results. All 43 analysed\\u000a genotypes were distinguishable by their band

My. Hassan Sedra; Philippe Lashermes; Pierre Trouslot; Marie-Christine Combes

1998-01-01

351

Detection of Low Genetic Variation in a Critically Endangered Chinese Pine, Pinus squamata , Using RAPD and ISSR Markers  

Microsoft Academic Search

With only 32 individuals in the northeastern corner of Yunnan Province, China, Pinus squamata is one of the most endangered conifers in the world. Using two classes of molecular markers, RAPD and ISSR, its very low\\u000a genetic variation was revealed. Shannon's index of phenotypic diversity (I) was 0.030, the mean effective number of alleles per locus (Ae) was 1.032, the

Zhi-Yong Zhang; Yong-Yan Chen; De-Zhu Li

2005-01-01

352

Determination of genetic stability in long-term micropropagated shoots of Pinus thunbergii Parl. using RAPD markers  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) markers were used to determine the genetic stability of long-term (more than 10 years)\\u000a micropropagated shoots of Japanese black pine (Pinus thunbergii Parl.). Thirty-six shoots consisting of three morphotypes (short, medium, and long needles) were randomly chosen from about\\u000a 4,000 micropropagated shoots regenerated from the explants of a single nematode-resistant mother plant. Out of 126

S. Goto; R. C. Thakur; K. Ishii

1998-01-01

353

Development of Reproducible EST-derived SSR Markers and Assessment of Genetic Diversity in Panax ginseng Cultivars and Related Species.  

PubMed

Little is known about the genetics or genomics of Panax ginseng. In this study, we developed 70 expressed sequence tag-derived polymorphic simple sequence repeat markers by trials of 140 primer pairs. All of the 70 markers showed reproducible polymorphism among four Panax speciesand 19 of them were polymorphic in six P. ginseng cultivars. These markers segregated 1:2:1 manner of Mendelian inheritance in an F2 population of a cross between two P. ginseng cultivars, 'Yunpoong' and 'Chunpoong', indicating that these are reproducible and inheritable mappable markers. A phylogenetic analysis using the genotype data showed three distinctive groups: a P. ginseng-P. japonicus clade, P. notoginseng and P. quinquefolius, with similarity coefficients of 0.70. P. japonicus was intermingled with P. ginseng cultivars, indicating that both species have similar genetic backgrounds. P. ginseng cultivars were subdivided into three minor groups: an independent cultivar 'Chunpoong', a subgroup with three accessions including two cultivars, 'Gumpoong' and 'Yunpoong' and one landrace 'Hwangsook' and another subgroup with two accessions including one cultivar, 'Gopoong' and one landrace 'Jakyung'. Each primer pair produced 1 to 4 bands, indicating that the ginseng genome has a highly replicated paleopolyploid genome structure. PMID:23717085

Choi, Hong-Il; Kim, Nam Hoon; Kim, Jun Ha; Choi, Beom Soon; Ahn, In-Ok; Lee, Joon-Soo; Yang, Tae-Jin

2011-11-01

354

Fecal source tracking in water by next-generation sequencing technologies using host-specific Escherichia coli genetic markers.  

PubMed

High levels of fecal bacteria are a concern for the aquatic environment, and identifying sources of those bacteria is important for mitigating fecal pollution and preventing waterborne disease. Escherichia coli has been used as an indicator of fecal pollution, however less success has been achieved using this organism for library-independent microbial source tracking. In this study, using next-generation sequencing technology we sequenced the whole genomes of 22 E. coli isolates from known sources (9 from humans, 2 from cows, 6 from pigs, and 5 from chickens) and identified candidate host-specific genomic regions. Specificity testing on the candidate regions was performed using 30 E. coli isolates from each source. Finally, we identified 4 human-, 2 cow-, 3 pig-, and 4 chicken-specific genetic markers useful for source tracking. We also found that a combination of multiplex PCR and dual index sequencing is effective for detecting multiple genetic markers in multiple isolates at one time. This technique was applied to investigating identified genetic markers in 549 E. coli isolates obtained from the Yamato River, Japan. Results indicate that humans constitute a major source of water contamination in the river. However, further work must include isolates obtained from geographically diverse animal hosts to make this method more reliable. PMID:25055157

Gomi, Ryota; Matsuda, Tomonari; Matsui, Yasuto; Yoneda, Minoru

2014-08-19

355

Genomics and genetics of gonadotropin beta-subunit genes: Unique FSHB and duplicated LHB/CGB loci  

PubMed Central

The follicle stimulating hormone (FSH), luteinizing hormone (LH) and chorionic gonadotropin (HCG) play a critical role in human reproduction. Despite the common evolutionary ancestry and functional relatedness of the gonadotropin hormone beta (GtHB) genes, the single-copy FSHB (at 11p13) and the multi-copy LHB/CGB genes (at 19q13.32) exhibit locus-specific differences regarding their genomic context, evolution, genetic variation and expressional profile. FSHB represents a conservative vertebrate gene with a unique function and it is located in a structurally stable gene-poor region. In contrast, the primate-specific LHB/CGB gene cluster is located in a gene-rich genomic context and demonstrates an example of evolutionary young and unstable genomic region. The gene cluster is shaped by a constant balance between selection that acts on specific functions of the loci and frequent gene conversion events among duplicons. As the transcription of the GtHB genes is rate-limiting in the assembly of respective hormones, the genomic and genetic context of the FSHB and the LHB/CGB genes largely affects the profile of the hormone production. PMID:20488225

Nagirnaja, Liina; Rull, Kristiina; Uusküla, Liis; Hallast, Pille; Grigorova, Marina; Laan, Maris

2010-01-01

356

Genetic structure in Orchesella cincta (Collembola): strong subdivision of European populations inferred from mtDNA and AFLP markers.  

PubMed

Population genetic structure is determined both by current processes and historical events. Current processes include gene flow, which is largely influenced by the migration capacity of a species. Historical events are, for example, glaciation periods, which have had a major impact on the distribution of many species. Species with a low capacity or tendency to move about or disperse often exhibit clear spatial genetic structures, whereas mobile species mostly show less spatial genetic differentiation. In this paper we report on the genetic structure of a small, wingless arthropod species (Orchesella cincta: Collembola) in Europe. For this purpose we used mtDNA COII sequences and AFLP markers. We show that large genetic differences exist between populations of O. cincta, as expected from O. cincta's winglessness and sedentary lifestyle. Despite the fact that most variability was observed within populations (59%), a highly significant amount of AFLP variation (25%) was observed between populations from northwestern Europe, central Europe and Italy. This suggests that gene flow among regions is extremely low, which is additionally supported by the lack of shared mtDNA alleles between regions. Based on the genetic variation and sequence differences observed we conclude that the subdivision occurred long before the last glaciation periods. Although the populations still interbreed in the lab, we assume that in the long term the genetic isolation of these regions may lead to speciation processes. PMID:15910323

Timmermans, M J T N; Ellers, J; Mariën, J; Verhoef, S C; Ferwerda, E B; VAN Straalen, N M

2005-06-01

357

Framing genetic risk: trust and credibility markers in online direct-to-consumer advertising for genetic testing  

Microsoft Academic Search

This study looks at Internet direct-to-consumer advertising (DTCA) for genetic testing to assess the way in which genetic risk information is framed to consumers, and strategies to establish trust and credibility in this context. Keywords specific to genetic test DTC advertising were entered into popular Internet search engines, arriving at 22 companies. Representations of benefits and risks on company websites

Edna F. Einsiedel; Rose Geransar

2009-01-01

358

Intra-population genetic diversity of cultivated carrot (Daucus carota L.) assessed by analysis of microsatellite markers.  

PubMed

Intra-population variation of 18 cultivated carrot (Daucus carota L. ssp. sativus) populations of diverse origins was evaluated using codominant microsatellite (SSR) markers. Using 27 genomic and EST-derived SSR markers, 253 alleles were identified with a mean 9.4 alleles per marker. Most of the alleles (60.5%) were rare i.e., with the frequency ? 0.05 while only 3.95% of alleles occurred with frequency > 0.6. EST-derived SSR markers were less polymorphic than genomic SSR markers. Differences in allele occurrence allowed 16 out of 18 populations to be assigned to either the Western or Asian carrot gene pools with high probability. Populations could be also discriminated due to the presence of private alleles (25.3% of all alleles). Most populations had excess of alleles in the homozygous state indicating their inbreeding, although heterozygous loci were common in F1 hybrids. Genetic diversity was due to allelic variation among plants within populations (62% of total variation) and between populations (38%). Accessions originating from continental Asia and Europe had more allelic variants and higher diversity than those from Japan and USA. Also, allelic richness and variability in landraces was higher than in F1 hybrids and open-pollinated cultivars. PMID:24432327

Maksylewicz, Anna; Baranski, Rafal

2013-01-01

359

Mechanisms and consequences of small supernumerary marker chromosomes: from Barbara McClintock to modern genetic-counseling issues.  

PubMed

Supernumerary marker chromosomes (SMCs) are common, but their molecular content and mechanism of origin are often not precisely characterized. We analyzed all centromere regions to identify the junction between the unique chromosome arm and the pericentromeric repeats. A molecular-ruler clone panel for each chromosome arm was developed and used for the design of a custom oligonucleotide array. Of 27 nonsatellited SMCs analyzed by array comparative genomic hybridization (aCGH) and/or fluorescence in situ hybridization (FISH), seven (approximately 26%) were shown to be unique sequence negative. Of the 20 unique-sequence-positive SMCs, the average unique DNA content was approximately 6.5 Mb (range 0.3-22.2 Mb) and 33 known genes (range 0-149). Of the 14 informative nonacrocentric SMCs, five (approximately 36%) contained unique DNA from both the p and q arms, whereas nine (approximately 64%) contained unique DNA from only one arm. The latter cases are consistent with ring-chromosome formation by centromere misdivision, as first described by McClintock in maize. In one case, a r(4) containing approximately 4.4 Mb of unique DNA from 4p was also present in the proband's mother. However, FISH revealed a cryptic deletion in one chromosome 4 and reduced alpha satellite in the del(4) and r(4), indicating that the mother was a balanced ring and deletion carrier. Our data, and recent reports in the literature, suggest that this "McClintock mechanism" of small-ring formation might be the predominant mechanism of origin. Comprehensive analysis of SMCs by aCGH and FISH can distinguish unique-negative from unique-positive cases, determine the precise gene content, and provide information on mechanism of origin, inheritance, and recurrence risk. PMID:18252220

Baldwin, Erin L; May, Lorraine F; Justice, April N; Martin, Christa L; Ledbetter, David H

2008-02-01

360

Genetic and biochemical markers of hydroxyurea therapeutic response in sickle cell anemia  

PubMed Central

Background Sickle cell anemia (SCA) presents a complex pathophysiology which can be affected by a number of modifying factors, including genetic and biochemical ones. In Brazil, there have been no studies verifying ?S-haplotypes effect on oxidative stress parameters. This study evaluated ?S-haplotypes and Hb F levels effects on oxidative stress markers and their relationship with hydroxyurea (HU) treatment in SCA patients. Methods The studied group was composed by 28 SCA patients. Thirteen of these patients were treated with HU and 15 of them were not. We used molecular methodology (PCR-RFLP) for hemoglobin S genotype confirmation and haplotypes identification. Biochemical parameters were measured using spectrophotometric methods (Thiobarbituric-acid-reactive substances and Trolox equivalent antioxidant capacity levels, catalase and GST activities) and plasma glutathione levels by High-performance liquid chromatography coupled to electrochemical detection. Results We found the highest frequency of Bantu haplotype (48.2%) which was followed by Benin (32.1%). We observed also the presence of Cameroon haplotype, rare in Brazilian population and 19.7% of atypical haplotypes. The protective Hb F effect was confirmed in SCA patients because these patients showed an increase in Hb F levels that resulted in a 41.3% decrease on the lipid peroxidation levels (r?=?0.74, p=0.01). Other biochemical parameters have not shown differential expression according to patient’s haplotypes. Bantu haplotype presence was related to the highest lipid peroxidation levels in patients (p?

2013-01-01

361

Genetic Structure of Lutzomyia longipalpis Populations in Mato Grosso Do Sul, Brazil, Based on Microsatellite Markers  

PubMed Central

Background Lutzomyialongipalpis (Diptera: Psychodidae) is the major vector of Leishmania (Leishmania) infantum and thus plays a crucial role in the epidemiology of American visceral leishmaniasis (AVL). This vector is the best studied species of sand fly in the Neotropical region. Many studies claim that this vector is in fact a species complex; however there is still no consensus regarding the number of species that belong into this complex or the geographical distribution of sibling species. The aim of the present study was to analyze the genetic relationships within Lu. longipalpis populations in the state of Mato Grosso do Sul (MS), Brazil. Methodology/Principal Findings We collected 30 Lu. longipalpis (15 females and 15 males) from five localities (Campo Grande, Três Lagoas, Aquidauana, Miranda and Bonito) and 30 Lu. Cruzi from Corumbá, totaling 180 sandflies from MS, and 30 Lu. longipalpis from Estrela de Alagoas, state of Alagoas (AL), Northeast Brazil. We show that eight previously described microsatellite loci were sufficient in distinguishing Lu. longipalpis from Lu. Cruzi, which is a closely related species, and in differentiating between Lu. longipalpis collected in MS versus Estrela de Alagoas. Analyses of the genotypes revealed introgression between sympatric Lu. longipalpis and Lu. Cruzi. Conclusions/Significance Our findings support the hypothesis of cryptic species within the Lu. longipalpis complex. Furthermore, our data revealed introgression between Lu. longipalpis and Lu. cruzi. This phenomenon should be further investigated to determine the level and incidence of hybridization between these two species. We also demonstrated that microsatellite markers are a powerful tool for differentiating sand fly populations and species. The present study has elucidated the population structure of Lu. longipalpis in MS and, by extension, the Neotropical Lu. longipalpis complex itself. PMID:24066129

Santos, Mirella F. C.; Ribolla, Paulo E. M.; Alonso, Diego P.; Andrade-Filho, José D.; Casaril, Aline E.; Ferreira, Alda M. T.; Fernandes, Carlos E. S.; Brazil, Reginaldo P.; Oliveira, Alessandra G.

2013-01-01

362

Bulinus species on Madagascar: molecular evolution, genetic markers and compatibility with Schistosoma haematobium.  

PubMed

Of the four species of Bulinus found on Madagascar, three species: B. obtusispira, B. liratus and B. bavayi are endemic while the fourth, B. forskalii, is probably a recent introduction from the African mainland. The evolutionary relationships of these species with Bulinus species from Africa were studied by phylogenetic analysis of DNA sequence variation at two mitochondrial loci: cytochrome oxidase subunit I (COI) and large ribosomal subunit (LSU) or 16S. The observed levels of nucleotide divergence within Bulinus were substantial but may underestimate the true levels as there was evidence of 'saturation' of transitional substitutions at both loci. A putative secondary structure model for the sequenced segment of the 16S was developed. Subsequent phylogenetic analysis using transversional changes only for both loci, showed that there were contrasting levels of divergence within the four species groups. B. obtusispira was consistently placed within the B. africanus group, appearing ancestral to this group and was closest to the basal node within Bulinus. Together with B. bavayi, the two species appear to have been isolated on Madagascar for a long time, contrasting with both B. liratus and B. forskalii that appear more recent colonisers; however, estimate of exact times of divergence is problematic. A PCR-RFLP assay was developed to enable identification and discrimination of B. obtusispira and B. liratus using discriminatory variation within the COI. To enable population genetic analysis within B. obtusispira, microsatellite markers were developed using an enrichment method and 8 primer pairs are reported. Laboratory infection experiments using Madasgacan S. haematobium from the Mahabo area showed that certain populations of B. obtusispira, B. liratus and B. bavayi were compatible. PMID:11769288

Stothard, J R; Brémond, P; Andriamaro, L; Sellin, B; Sellin, E; Rollinson, D

2001-01-01

363

The Unique Transcriptional Activation Domain of Nuclear Factor-I-X3 Is Critical to Specifically Induce Marker Gene Expression in Astrocytes*  

PubMed Central

Transcription factors of the nuclear factor 1 (NFI) family regulate normal brain development in vertebrates. However, multiple splice variants of four NFI isoforms exist, and their biological functions have yet to be elucidated. Here, we cloned and analyzed human NFI-X3, a novel splice variant of the nfix gene, which contains a unique transcriptional activation (TA) domain completely conserved in primates. In contrast to previously cloned NFI-X1, overexpression of NFI-X3 potently activates NFI reporters, including glial fibrillary acidic protein (GFAP) reporter, in astrocytes and glioma cells. The GAL4 fusion protein containing the TA domain of NFI-X3 strongly activates the GAL4 reporter, whereas the TA domain of NFI-X1 is ineffective. The expression of NFI-X3 is dramatically up-regulated during the differentiation of neural progenitors to astrocytes and precedes the expression of astrocyte markers, such as GFAP and SPARCL1 (Secreted Protein, Acidic and Rich in Cysteines-like 1). Overexpression of NFI-X3 dramatically up-regulates GFAP and SPARCL1 expression in glioma cells, whereas the knockdown of NFI-X3 diminishes the expression of both GFAP and SPARCL1 in astrocytes. Although activation of astrocyte-specific genes involves DNA demethylation and subsequent increase of histone acetylation, NFI-X3 activates GFAP expression, in part, by inducing alterations in the nucleosome architecture that lead to the increased recruitment of RNA polymerase II. PMID:21189253

Singh, Sandeep K.; Wilczynska, Katarzyna M.; Grzybowski, Adrian; Yester, Jessie; Osrah, Bahiya; Bryan, Lauren; Wright, Sarah; Griswold-Prenner, Irene; Kordula, Tomasz

2011-01-01

364

Development and amplification of multiple co-dominant genetic markers from single spores of arbuscular mycorrhizal fungi by nested multiplex PCR  

Microsoft Academic Search

Multiple co-dominant genetic markers from single spores of the arbuscular mycorrhizal (AM) fungi Glomus mosseae, Glomus caledonium, and Glomus geosporum were amplified by nested multiplex PCR using a combination of primers for simultaneous amplification of five loci in one PCR. Subsequently, each marker was amplified separately in nested PCR using specific primers. Polymorphic loci within the three putative single copy

Eva H. Stukenbrock; Søren Rosendahl

2005-01-01

365

Genetic analysis of Spanish melon ( Cucumis melo L.) germplasm using a standardized molecular-marker array and geographically diverse reference accessions  

Microsoft Academic Search

Genetic relationships among 125 Spanish melon ( Cucumis melo L.) accessions from a Spanish germplasm collection were assessed using a standard molecular-marker array consisting of 34 random amplified polymorphic DNA (RAPD) markers bands (19 primers) and 72 reference accessions drawn from previous studies. The reference accession array consisted of a broad range [Japanese (19) Crete (17), African (15), and USA

A. I. López-Sesé; J. E. Staub; M. L. Gómez-Guillamón

2003-01-01

366

Identification of Single-Copy Orthologous Genes between Physalis and Solanum lycopersicum and Analysis of Genetic Diversity in Physalis Using Molecular Markers  

PubMed Central

The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei’s genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis. PMID:23166835

Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai

2012-01-01

367

[Genetic structure and genetic diversity of Artemisia annua varieties (strains) populations based on SCoT markers].  

PubMed

To reveal the genetic diversity and genetic structure in Artemisia annua varieties (strains) populations, we detected the genetic polymorphism within and among eight varieties (strains) populations (192 individuals) by the approach of Start Codon Targeted Polymorphism (SCoT). The associated genetic parameters were calculated by POPGENE1.31 and the relationship was constructed based on UPGMA method. The results showed that, using 20 screened primers, a total of 145 bands were produced, of which 122 were polymorphic loci. At species level, there was a high level of genetic diversity among eight varieties (strains) populations (PPB = 84.1% ,H = 0.217 3 and H(sp) = 0.341 9). However, at the variety (strains) population level, genetic diversity was lower, the average of genetic parameters was PPB = 41.9%, H = 0.121 5, H(pop) = 0.186 8. The Nei's genetic differentiation coefficient was 0.441 0, indicate that most of the genetic variation in this species existed within the variety populations. The gene flow (N(m) = 0.633 9) was less among populations, indicating that the degree of genetic differentiation was higher. Genetic similarity coefficient were changed from 0.755 1 to 0.985 7. By clustering analysis, eight varieties (strains) were clustered into two major categories and it was also showed the same or similar genetic background varieties (strains) have a tendency to gather in the same group. Results suggest that, in variety breeding, breeders should strengthen the exchange of bred germplasm and increase mutual penetration of excellent genes, which would broaden the genetic base of A. annua. PMID:25522606

Chen, Da-xia; Cui, Guang-lin; Zhang, Xue; Li, Long-yun

2014-09-01

368

Study of genetic variation in sesame (Sesamum indicum L.) using agro-morphological traits and ISSR markers.  

PubMed

This research was conducted to study the genetic variation among eighteen genotypes of sesame (Sesamum indicum L.) collected from various agro-climatic regions of Iran along with six exotic genotypes from the Asian countries using both agro-morphological and ISSR marker traits. The results showed significant differences among genotypes for all agro-morphological traits and a relatively high genetic coefficient of variation observed for number of fruiting branches per plant, capsules per plant, plant height and seed yield per plant. Cluster analysis based on these traits grouped the genotypes into five separate clusters. Larger inter- than intra cluster distances implies the presence of higher genetic variability between the genotypes of different groups. Genotypes of two clusters with a good amount of genetic divergence and desirable agronomic traits were detected as promising genotypes for hybridization programs. The 13 ISSR primers chosen for molecular analysis revealed 170 bands, of which 130 (76.47%) were polymorphic. The generated dendrogram based on ISSR profiles divided the genotypes into seven groups. A principal coordinate analysis confirmed the results of clustering. The agro-morphological traits and ISSR markers reflected different aspects of genetic variation among the genotypes as revealed by a non significant cophenetic correlation in the Mantel test. Therefore the complementary application of both types of information is recommended to maximize the efficiency of sesame breeding programs. The discordance among diversity patterns and geographical distribution of genotypes found in this investigation implies that the parental lines for hybridization should be selected based on genetic diversity rather than the geographical distribution. PMID:21539180

Parsaeian, M; Mirlohi, A; Saeidi, G

2011-03-01

369

Genetic Structure and Inferences on Potential Source Areas for Bactrocera dorsalis (Hendel) Based on Mitochondrial and Microsatellite Markers  

PubMed Central

Bactrocera dorsalis (Diptera: Tephritidae) is mainly distributed in tropical and subtropical Asia and in the Pacific region. Despite its economic importance, very few studies have addressed the question of the wide genetic structure and potential source area of this species. This pilot study attempts to infer the native region of this pest and its colonization pathways in Asia. Combining mitochondrial and microsatellite markers, we evaluated the level of genetic diversity, genetic structure, and the gene flow among fly populations collected across Southeast Asia and China. A complex and significant genetic structure corresponding to the geographic pattern was found with both types of molecular markers. However, the genetic structure found was rather weak in both cases, and no pattern of isolation by distance was identified. Multiple long-distance dispersal events and miscellaneous host selection by this species may explain the results. These complex patterns may have been influenced by human-mediated transportation of the pest from one area to another and the complex topography of the study region. For both mitochondrial and microsatellite data, no signs of bottleneck or founder events could be identified. Nonetheless, maximal genetic diversity was observed in Myanmar, Vietnam and Guangdong (China) and asymmetric migration patterns were found. These results provide indirect evidence that the tropical regions of Southeast Asia and southern coast of China may be considered as the native range of the species and the population expansion is northward. Yunnan (China) is a contact zone that has been colonized from different sources. Regions along the southern coast of Vietnam and China probably served to colonize mainly the southern region of China. Southern coastal regions of China may also have colonized central parts of China and of central Yunnan. PMID:22615898

Shi, Wei; Kerdelhué, Carole; Ye, Hui

2012-01-01

370

Genetic Diversity and Population Structure in Native Chicken Populations from Myanmar, Thailand and Laos by Using 102 Indels Markers  

PubMed Central

The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels) markers. Most of the indels loci were polymorphic (71% to 96%), and the genetic variability was similar in all populations. The average observed heterozygosities (HO) and expected heterozygosities (HE) ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst) for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088) than Myanmar (0.041) and Laotian (0.024) populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ) tree, using Nei’s genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3) from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens. PMID:25557671

Maw, A. A.; Kawabe, K.; Shimogiri, T.; Rerkamnuaychoke, W.; Kawamoto, Y.; Masuda, S.; Okamoto, S.

2015-01-01

371

Identification and characterization of dinucleotide repeat (CA)[sub n] markers for genetic mapping in dog  

SciTech Connect

A large block of simple sequence repeat (SSR) polymorphisms for the dog genome has been isolated and characterized. Screening of primary libraries by conventional hybridization methods as well as by screening of enriched marker-selected libraries led to the isolation of a large number of genomic clones that contained (CA)[sub n] repeats. The sequences of 101 clones showed that the size and complexity of (CA)[sub n] repeats in the dog genome were similar to those reported for these markers in the human genome. Detailed analysis of a representative subset of these markers revealed that most markers were moderately to highly polymorphic, with PIC values exceeding 0.70 for 33% of the markers tested. An association between higher PIC values and markers containing longer (CA)[sub n] repeats was observed in these studies, as previously noted for similar markers in the human genome. A list of primer sequences that tag each characterized marker is provided, and a comprehensive system of nomenclature for the dog genome is suggested. 28 refs., 4 figs., 2 tabs.

Ostrander, E.A. (Lawrence Berkeley Lab., CA (United States)); Sprague, G.F. Jr. (Univ. of Oregon, Eugene (United States)); Rine, J. (Lawrence Berkeley Lab., CA (United States) Univ. of California, Berkeley (United States))

1993-04-01

372

Exploring the Genetic Characteristics of Two Recombinant Inbred Line Populations via High-Density SNP Markers in Maize  

PubMed Central

Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43–11.50 cM/Mb while the minimum was 0.08–0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop. PMID:23300772

Pan, Qingchun; Ali, Farhan; Yang, Xiaohong; Li, Jiansheng; Yan, Jianbing

2012-01-01

373

A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers.  

PubMed Central

Three linkage maps of the genome of the microhymenopteran Trichogramma brassicae were constructed from the analysis of segregation of random amplified polymorphic DNA markers in three F2 populations. These populations were composed of the haploid male progeny of several virgin F1 females, which resulted from the breeding of four parental lines that were nearly fixed for different random amplified polymorphic DNA markers and that were polymorphic for longevity and fecundity characters. As the order of markers common to the three mapping populations was found to be well conserved, a composite linkage map was constructed. Eighty-four markers were organized into five linkage groups and two pairs. The mean interval between two markers was 17.7 cM, and the map spanned 1330 cM. PMID:9725846

Laurent, V; Wajnberg, E; Mangin, B; Schiex, T; Gaspin, C; Vanlerberghe-Masutti, F

1998-01-01

374

Exploration of genetic diversity among medicinally important genus Epimedium species based on genomic and EST-SSR marker.  

PubMed

Epimedium species has gained prime importance due to their medicinal and economic values. Therefore, in this study, 26 genomic SSR and 10 EST-SSR markers were developed for 13 medicinal species of the Epimedium genus and one out-group species Vancouveria hexandra W. J. Hooker to explore the existing genetic diversity. A total of 100 alleles by genomic SSR and 65 by EST-SSR were detected. The genomic SSR markers were presented between 2-7 alleles per locus. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 4.5 and 0.0254 to 2.8108, respectively. Similarly, for EST-SSR, these values were ranged from 3.00 to 4.00 and 1.9650 to 2.7142. The number of alleles for EST-SSR markers ranged from 3 to 10 with an average of 3.51 per loci. It has been concluded that medicinally important species of the genus Epimedium possesses lower intraspecific genetic variation. PMID:25421361

Yousaf, Zubaida; Hu, Weiming; Zhang, Yanjun; Zeng, Shaohua; Wang, Ying

2014-11-25

375

Genetic variation in Staphylococcus aureus coagulase genes: potential and limits for use as epidemiological marker.  

PubMed Central

To perform coagulase gene typing, the repeated units encoding hypervariable regions of the Staphylococcus aureus coagulase gene were amplified by the PCR technique; this was followed by AluI restriction enzyme digestion and analysis of restriction fragment length polymorphism (RFLP) patterns. In order to assess the discriminatory power of this typing method, 30 epidemiologically unrelated S. aureus strains which differed by their pulsed-field gel electrophoresis patterns were examined. Although 18 of the 30 strains had unique and unshared AluI RFLP patterns, there were only four observed patterns in the remaining 12 strains. This finding indicated that unrelated strains may share identical AluI RFLP patterns. To elucidate the degree of genetic variation in the C-terminus-encoding loci within the coagulase genes, the PCR products of these 12 strains were subjected to Taq polymerase-mediated sequencing. Sequence analysis confirmed the AluI recognition sites in each of the four RFLP groups and demonstrated that AluI appears to yield the highest RFLP in restriction enzyme analysis. By their DNA sequences the majority of strains sharing common AluI groups could be clearly differentiated from each other and revealed between 93.2 and 98.5% homology. When we determined the nucleotide sequences of two strains after six subcultivations no significant alterations were observed. Because the discriminatory power of the current coagulase gene typing method is not great enough to be used as the sole method to type S. aureus, additional techniques are necessary. Sequence analysis of the repeated unit-encoding region for the typing of S. aureus may be potentially useful as an alternative to other current molecular typing techniques. Images PMID:7814475

Schwarzkopf, A; Karch, H

1994-01-01

376

Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape  

PubMed Central

Background The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. Results We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. Conclusions The comprehensive molecular characterization of our grape germplasm collection contributes to the knowledge about levels and distribution of genetic diversity in the existing resources of Vitis and provides insights into genetic subdivision within the European germplasm. Genotypic and phenotypic information compared in this study may efficiently guide further exploration of this diversity for facilitating its practical use. PMID:23497049

2013-01-01

377

Tissue-specifically regulated site-specific excision of selectable marker genes in bivalent insecticidal, genetically-modified rice.  

PubMed

Marker-free, genetically-modified rice was created by the tissue-specifically regulated Cre/loxP system, in which the Cre recombinase gene and hygromycin phosphotransferase gene (hpt) were flanked by two directly oriented loxP sites. Cre expression was activated by the tissue-specific promoter OsMADS45 in flower or napin in seed, resulting in simultaneous excision of the recombinase and marker genes. Segregation of T1 progeny was performed to select recombined plants. The excision was confirmed by PCR, Southern blot and sequence analyses indicating that efficiency varied from 10 to 53 % for OsMADS45 and from 12 to 36 % for napin. The expression of cry1Ac and vip3A was detected by RT-PCR analysis in marker-free transgenic rice. These results suggested that our tissue-specifically regulated Cre/loxP system could auto-excise marker genes from transgenic rice and alleviate public concerns about the security of GM crops. PMID:23974493

Hu, Zhan; Ding, Xuezhi; Hu, Shengbiao; Sun, Yunjun; Xia, Liqiu

2013-12-01

378

A LCP 85-384 genetic linkage map enriched with polymorphic SSR markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Sugarcane (Saccharum spp. hybrids) cultivars, such as Q165, R570 and LCP 85-384, have been used to construct genetic segregation populations for the development of genetic linkage maps. Based on the genetic linkage map for a selfed-progeny population of R570, the French research group at CIRAD tagge...

379

Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers.  

PubMed

Twelve different Ty1-copia and Ty3-gypsy group LTR retrotransposons were compared for their usefulness in SSAP marker development in two agriculturally important Vicia species. Three of the retrotransposons, PDR1, Tps19 and Tvf4, yielded useful SSAP marker systems in V. faba, and V. narbonensis. Another, Tvf1 was a good source of SSAP markers in V. narbonensis alone. The optimized SSAP marker systems were applied to the analysis of two diverse Vicia germplasm sets. Two hundred and two polymorphic Tvf1 SSAP markers were scored in 56 V. narbonensis samples and 196 polymorphic markers derived from the other three most useful retrotransposons were scored in a collection of 20 V. faba samples. The marker data were then used to construct phylogenetic trees. The trees for both species tend to show long-branch lengths, with rather little fine structure. Some V. narbonensis accessions cluster by geographical origin but many do not and a given geographical region is often represented by multiple diverse groups in the tree, suggesting a deep and ancient structure for the diversity of V. narbonensis that spans its current geographic range. The tree for the V. faba accessions also shows very limited clustering with geographical origin and no obvious correlation between diversity and morphology-based taxonomic groupings for the species. PMID:17576596

Sanz, Alberto Martín; Gonzalez, Susana Gilsanz; Syed, Naeem Hasan; Suso, Maria Jose; Saldaña, Constantino Caminero; Flavell, Andrew J

2007-10-01

380

Molecular Markers for the Classification of Switchgrass ( Panicum virgatum L.) Germplasm and to Assess Genetic Diversity in Three Synthetic Switchgrass Populations  

Microsoft Academic Search

Information regarding the amount of genetic diversity is necessary to enhance the effectiveness of breeding programs and germplasm conservation efforts. Genetic variation between 21 switchgrass genotypes randomly selected from two lowland (‘Alamo’ and ‘Kanlow’) and one upland (‘Summer’) synthetic cultivars were estimated using restriction fragment length polymorphism (RFLP) markers. Comparison of 85 RFLP loci revealed 92% polymorphism between at least

Ali M. Missaoui; Andrew H. Paterson; Joseph H. Bouton

2006-01-01

381

Using microsatellite (SSR) and morphological markers to assess the genetic diversity of 12 falcata (Medicago sativa spp. falcata) populations from Eurasia  

Microsoft Academic Search

Falcata (Medicago sativa spp. falcata L.), with its high resistance to cold weather, drought and disease, plays an important role in alfalfa breeding. The aim of this study was to assess the genetic diversity of the 12 falcata populations in Eurasia using SSR markers and morphological traits. Regressions for genetic distance, phenotypic distance and geographic distance were also computed to

Ping Li; Yunwen Wang; Xiaolong Sun; Jianguo Han

382

Assessment of genetic diversity among African cassava Manihot esculenta Grantz accessions resistant to the cassava mosaic virus disease using SSR markers  

Microsoft Academic Search

A study was conducted to determine the extent of genetic diversity among African cassava (Manihot esculenta Crantz) accessions resistant to the cassava mosaic virus disease (CMD), using simple sequence repeat (SSR) markers. The accessions included a breeding stock (clone 58308), five improved lines, 62 CMD resistant and 10 CMD susceptible landraces. Genetic diversity was assessed among accessions in five cluster

Yvonne Lokko; Alfred Dixon; Sam Offei; Eric Danquah; Martin Fregene

2006-01-01

383

Genetic variation and phylogenetic relationships among worldwide collections of the Russian wheat aphid, Diuraphis noxia (Mordvilko), inferred from allozyme and RAPD-PCR markers  

Microsoft Academic Search

Genetic analyses were conducted on Diuraphis noxia (Mordvilko) populations collected from wheat, barley and other grasses from various countries throughout the world. These collections had been found to contain clones that differed in virulence from various cultivars, cuticular hydrocarbon profiles and life cycle characters. Discrete genetic markers analysed in this study included allozymes and arbitrary regions of the genome amplified

G J Puterka; W C Black; W M Steiner; R L Burton

1993-01-01

384

Medical Genetic Polymorphisms as Markers of Evolutionary Forces Within the Human Genome: Hypotheses Focusing on Natural Selection in the Basque Population  

Microsoft Academic Search

Natural selection, drift, and gene flow are the three major evolutionary forces at the origin of genetic diversity among human populations. To further explore these mechanisms, we present an innovative approach using various medical genetic markers and focusing on the Basque population. From this study we can confirm the important role of drift in this endogamous human group and can

Frédéric Bauduer; Anna Degioanni; Olivier Dutour

2009-01-01

385

Genetic Population Structure and Mixed-Stock Analysis of Walleyes in the Lake Erie–Lake Huron Corridor using Allozyme and Mitochondrial DNA Markers  

Microsoft Academic Search

We used allozymes and mitochondrial DNA (mtDNA) restriction fragment length polymorphisms to determine if spawning populations of walleyes Stizostedion vitreum from the Lake Erie–Lake Huron corridor are genetically differentiated and to estimate their contributions to a commercial fishery in southern Lake Huron (operated by Purdy Fisheries) in 1994 and 1995. Both types of genetic markers detected significant differentiation among walleyes

Tara L. McParland; Moira M. Ferguson; Arunas P. Liskauskas

1999-01-01

386

Genetic diversity, genetic structure and demographic history of Cycas simplicipinna (Cycadaceae) assessed by DNA sequences and SSR markers  

PubMed Central

Background Cycas simplicipinna (T. Smitinand) K. Hill. (Cycadaceae) is an endangered species in China. There were seven populations and 118 individuals that we could collect were genotyped in this study. Here, we assessed the genetic diversity, genetic structure and demographic history of this species. Results Analyses of data of DNA sequences (two maternally inherited intergenic spacers of chloroplast, cpDNA and one biparentally inherited internal transcribed spacer region ITS4-ITS5, nrDNA) and sixteen microsatellite loci (SSR) were conducted in the species. Of the 118 samples, 86 individuals from the seven populations were used for DNA sequencing and 115 individuals from six populations were used for the microsatellite study. We found high genetic diversity at the species level, low genetic diversity within each of the seven populations and high genetic differentiation among the populations. There was a clear genetic structure within populations of C. simplicipinna. A demographic history inferred from DNA sequencing data indicates that C. simplicipinna experienced a recent population contraction without retreating to a common refugium during the last glacial period. The results derived from SSR data also showed that C. simplicipinna underwent past effective population contraction, likely during the Pleistocene. Conclusions Some genetic features of C. simplicipinna such as having high genetic differentiation among the populations, a clear genetic structure and a recent population contraction could provide guidelines for protecting this endangered species from extinction. Furthermore, the genetic features with population dynamics of the species in our study would help provide insights and guidelines for protecting other endangered species effectively. PMID:25016306

2014-01-01

387

Characterization of admixture in an urban sample from Buenos Aires, Argentina, using uniparentally and biparentally inherited genetic markers.  

PubMed

In this study we analyzed a sample of the urban population of La Plata, Argentina, using 17 mtDNA haplogroups, the DYS 199 Y-chromosome polymorphism, and 5 autosomal population-associated alleles (PAAs). The contribution of native American maternal lineages to the population of La Plata was estimated as 45.6%, whereas the paternal contribution was much lower (10.6%), clearly indicating directional mating. Regarding autosomal evidence of admixture, the relative European, native American, and West African genetic contributions to the gene pool of La Plata were estimated to be 67.55% (+/-2.7), 25.9% (+/-4.3), and 6.5% (+/-6.4), respectively. When admixture was calculated at the individual level, we found a low correlation between the ancestral contribution estimated with uniparental lineages and autosomal markers. Most of the individuals from La Plata with a native American mtDNA haplogroup or the DYS199*T native American allele show a genetic contribution at the autosomal level that can be traced primarily to Europe. The results of this study emphasize the need to use both uniparentally and biparentally inherited genetic markers to understand the history of admixed populations. PMID:15754971

Martínez Marignac, Veronica L; Bertoni, Bernardo; Parra, Esteban J; Bianchi, Néstor O

2004-08-01

388

Population genetics of invasive Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species in the United States based on microsatellite markers.  

PubMed

The Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) cryptic species complex of whiteflies contains two species, MEAM1 and MED, that are highly invasive in supportive climates the world over. In the United States, MEAM1 occurs both in the field and in the greenhouse, but MED is only found in the greenhouse. To make inferences about the population structure of both species, and the origin and recent spread of MED within the United States, 987 MEAM1 whiteflies and 340 MED whiteflies were genotyped at six and seven microsatellite loci, respectively, for population genetic analyses. Major results of the study are 1) MED exhibits more population structure and genetic differentiation than MEAM1, 2) nuclear microsatellite markers exhibit a high degree of concordance with mitochondrial markers recovering a major east-west phylogeographic break within MED, 3) both eastern and western MED are found throughout the continental United States and eastern MED is present in Hawaii, and 4) MEAM1 contains two greenhouse U.S. populations significantly differentiated from other U.S. MEAM1. The results suggest that MED was introduced into the United States on at least three occasions and rapidly spread throughout the United States, showing no discernible differentiation across 7,000 km. The results further suggest that there is an enhanced role of the protected agricultural environment in promoting genetic differentiation in both invasive B. tabaci cryptic species. PMID:23865202

Dickey, Aaron M; Osborne, Lance S; Shatters, Robert G; Hall, Paula A M; Mckenzie, Cindy L

2013-06-01

389

Microsatellite markers from the 'South American fruit fly' Anastrepha fraterculus: a valuable tool for population genetic analysis and SIT applications  

PubMed Central

Background Anastrepha fraterculus Wiedemann is a horticultural pest which causes significant economic losses in the fruit-producing areas of the American continent and limits the access of products to international markets. The use of environmentally friendly control strategies against this pest is constrained due to the limited knowledge of its population structure. Results We developed microsatellite markers for A. fraterculus from four genomic libraries, which were enriched in CA, CAA, GA and CAT microsatellite motifs. Fifty microsatellite regions were evaluated and 14 loci were selected for population genetics studies. Genotypes of 122 individuals sampled from four A. fraterculus populations were analyzed. The level of polymorphism ranged from three to 13 alleles per locus and the mean expected heterozygosity ranged from 0.60 to 0.64. Comparison between allelic and genotypic frequencies showed significant differences among all pairs of populations. Conclusions This novel set of microsatellite markers provides valuable information for the description of genetic variability and population structure of wild populations and laboratory strains of A. fraterculus. This information will be used to identify and characterize candidate strains suitable to implement effective pest control strategies and might represent a first step towards having a more comprehensive knowledge about the genetics of this pest. PMID:25471285

2014-01-01

390

Genetic mapping, marker assisted selection and allelic relationships for the Pu 6 gene conferring rust resistance in sunflower.  

PubMed

Rust resistance in the sunflower line P386 is controlled by Pu 6 , a gene which was reported to segregate independently from other rust resistant genes, such as R 4 . The objectives of this work were to map Pu 6 , to provide and validate molecular tools for its identification, and to determine the linkage relationship of Pu 6 and R 4 . Genetic mapping of Pu 6 with six markers covered 24.8 cM of genetic distance on the lower end of linkage Group 13 of the sunflower consensus map. The marker most closely linked to Pu 6 was ORS316 at 2.5 cM in the distal position. ORS316 presented five alleles when was assayed with a representative set of resistant and susceptible lines. Allelism test between Pu 6 and R 4 indicated that both genes are linked at a genetic distance of 6.25 cM. This is the first confirmation based on an allelism test that at least two members of the R adv /R 4 /R 11 / R 13a /R 13b /Pu 6 cluster of genes are at different loci. A fine elucidation of the architecture of this complex locus will allow designing and constructing completely new genomic regions combining genes from different resistant sources and the elimination of the linkage drag around each resistant gene. PMID:25320555

Bulos, Mariano; Vergani, Pablo Nicolas; Altieri, Emiliano

2014-09-01

391

Genetic transformation of the tomato pathogen Pyrenochaeta lycopersici allowed gene knockout using a split-marker approach.  

PubMed

Pyrenochaeta lycopersici, as other soil-transmitted fungal pathogens, generally received little attention compared to the pathogens affecting the aerial parts of the plants, although causing stunt and important fruit yield reduction of agronomic relevant crops. The scope of this study was to develop a system allowing to investigate the functional role of P. lycopersici genes putatively involved in the corky root rot of tomato. A genetic transformation system based on a split-marker approach was developed and tested to knock out a P. lycopersici gene encoding for a lytic polysaccharide monooxygenase (Plegl1) induced during the disease development. The regions flanking Plegl1 gene were fused with the overlapping parts of hygromycin marker gene, to favour homologous recombination. We were able to obtain four mutants not expressing the Plegl1 gene though, when tested on a susceptible tomato cultivar, Plegl1 mutants showed unaltered virulence, compared with the wild-type strain. The strategy illustrated in the present work demonstrated for the first time that homologous recombination occurs in P. lycopersici. Moreover, a transformation system mediated by Agrobacterium tumefaciens was established and stable genetic transformants have been obtained. The transformation systems developed represent important tools for investigating both the role of genes putatively involved in P. lycopersici interaction with host plant and the function of other physiological traits which emerged to be genetically expanded from the recent genome sequencing of this fungus. PMID:25413737

Aragona, Maria; Valente, Maria Teresa

2014-11-21

392

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity  

PubMed Central

Background Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to develop efficient strategies to use short-read length platforms for de novo assembly and marker development. The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms. Results A de novo assembly of transcriptome sequence from four genetic backgrounds produced 58,751 contigs and singletons. Over 50% of these assembled sequences were annotated allowing detection of transposable elements and new carrot anthocyanin genes. Presence of multiple genetic backgrounds in our assembly allowed the identification of 114 computationally polymorphic SSRs, and 20,058 SNPs at a depth of coverage of 20× or more. Polymorphisms were predominantly between inbred lines except for the cultivated x wild RIL pool which had high intra-sample polymorphism. About 90% and 88% of tested SSR and SNP primers amplified a product, of which 70% and 46%, respectively, were of the expected size. Out of verified SSR and SNP markers 84% and 82% were polymorphic. About 25% of SNPs genotyped were polymorphic in two diverse mapping populations. Conclusions This study confirmed the potential of short read platforms for de novo EST assembly and identification of genetic polymorphisms in carrot. In addition we produced the first large-scale transcriptome of carrot, a species lacking genomic resources. PMID:21810238

2011-01-01

393

Genetic mapping, marker assisted selection and allelic relationships for the Pu6 gene conferring rust resistance in sunflower  

PubMed Central

Rust resistance in the sunflower line P386 is controlled by Pu6, a gene which was reported to segregate independently from other rust resistant genes, such as R4. The objectives of this work were to map Pu6, to provide and validate molecular tools for its identification, and to determine the linkage relationship of Pu6 and R4. Genetic mapping of Pu6 with six markers covered 24.8 cM of genetic distance on the lower end of linkage Group 13 of the sunflower consensus map. The marker most closely linked to Pu6 was ORS316 at 2.5 cM in the distal position. ORS316 presented five alleles when was assayed with a representative set of resistant and susceptible lines. Allelism test between Pu6 and R4 indicated that both genes are linked at a genetic distance of 6.25 cM. This is the first confirmation based on an allelism test that at least two members of the Radv/R4/R11/ R13a/R13b/Pu6 cluster of genes are at different loci. A fine elucidation of the architecture of this complex locus will allow designing and constructing completely new genomic regions combining genes from different resistant sources and the elimination of the linkage drag around each resistant gene. PMID:25320555

Bulos, Mariano; Vergani, Pablo Nicolas; Altieri, Emiliano

2014-01-01

394

Development of microsatellite markers in the branched broomrape Phelipanche ramosa L. (Pomel) and evidence for host-associated genetic divergence.  

PubMed

Phelipanche ramosa is a parasitic plant that infects numerous crops worldwide. In Western Europe it recently expanded to a new host crop, oilseed rape, in which it can cause severe yield losses. We developed 13 microsatellite markers for P. ramosa using next-generation 454 sequencing data. The polymorphism at each locus was assessed in a sample of 96 individuals collected in France within 6 fields cultivated with tobacco, hemp or oilseed rape. Two loci were monomorphic. At the other 11 loci, the number of alleles and the expected heterozygosity ranged from 3 to 6 and from 0.31 to 0.60, respectively. Genetic diversity within each cultivated field was very low. The host crop from which individuals were collected was the key factor structuring genetic variation. Individuals collected on oilseed rape were strongly differentiated from individuals collected on hemp or tobacco, which suggests that P. ramosa infecting oilseed rape forms a genetically diverged race. The microsatellites we developed will be useful for population genetics studies and for elucidating host-associated genetic divergence in P. ramosa. PMID:24419096

Le Corre, Valérie; Reibel, Carole; Gibot-Leclerc, Stéphanie

2014-01-01

395

Inferring population structure and genetic diversity of broad range of wild diploid alfalfa (Medicago sativa L.) accessions using SSR markers.  

PubMed

Diversity analyses in alfalfa have mainly evaluated genetic relationships of cultivated germplasm, with little known about variation in diploid germplasm in the M. sativa-falcata complex. A collection of 374 individual genotypes derived from 120 unimproved diploid accessions from the National Plant Germplasm System, including M. sativa subsp. caerulea, falcata, and hemicycla, were evaluated with 89 polymorphic SSR loci in order to estimate genetic diversity, infer the genetic bases of current morphology-based taxonomy, and determine population structure. Diploid alfalfa is highly variable. A model-based clustering analysis of the genomic data identified two clearly discrete subpopulations, corresponding to the morphologically defined subspecies falcata and caerulea, with evidence of the hybrid nature of the subspecies hemicycla based on genome composition. Two distinct subpopulations exist within each subsp. caerulea and subsp. falcata. The distinction of caerulea was based on geographical distribution. The two falcata groups were separated based on ecogeography. The results show that taxonomic relationships based on morphology are reflected in the genetic marker data with some exceptions, and that clear distinctions among subspecies are evident at the diploid level. This research provides a baseline from which to systematically evaluate variability in tetraploid alfalfa and serves as a starting point for exploring diploid alfalfa for genetic and breeding experiments. PMID:20352180

Sakiro?lu, Muhammet; Doyle, Jeffrey J; Charles Brummer, E

2010-08-01

396

Genetic diversity of an Azorean endemic and endangered plant species inferred from inter-simple sequence repeat markers.  

PubMed

Knowledge of the levels and distribution of genetic diversity is important for designing conservation strategies for threatened and endangered species so as to guarantee sustainable survival of populations and to preserve their evolutionary potential. Picconia azorica is a valuable Azorean endemic species recently classified as endangered. To contribute with information useful for the establishment of conservation programmes, the genetic variability and differentiation among 230 samples from 11 populations collected in three Azorean islands was accessed with eight inter-simple sequence repeat markers. A total of 64 polymorphic loci were detected. The majority of genetic variability was found within populations and no genetic structure was detected between populations and between islands. Also the coefficient of genetic differentiation and the level of gene flow indicate that geographical distances do not act as barriers for gene flow. In order to ensure the survival of populations in situ and ex situ management practices should be considered, including artificial propagation through the use of plant tissue culture techniques, not only for the restoration of habitat but also for the sustainable use of its valuable wood. PMID:24969504

Lopes, Maria S; Mendonça, Duarte; Bettencourt, Sílvia X; Borba, Ana R; Melo, Catarina; Baptista, Cláudio; da Câmara Machado, Artur

2014-01-01

397

Detection of genetic variation between and within populations of Gliricidia sepium and G. maculata using RAPD markers.  

PubMed

Gliricidia sepium and G. maculata are multi-purpose leguminous trees native to Central America and Mexico. Research programmes have been initiated to define the native distribution of Gliricidia and sample the spectrum of genetic variation. To date, there has been little systematic assessment of genetic variability in multi-purpose tree species. Accurate estimates of diversity between- and within-populations are considered a prerequisite for the optimization of sampling and breeding strategies. We have used a PCR-based polymorphic assay procedure (RAPDs) to monitor genetic variability in Gliricidia. Extensive genetic variability was detected between species and the variability was partitioned into between- and within-population components. On average, most (60 per cent) of the variation occurs between G. sepium populations but oligonucleotide primers differed in their capacity to detect variability between and within populations. Population-specific genetic markers were identified. RAPDs provide a cost-effective method for the precise and routine evaluation of variability and may be used to identify areas of maximum diversity. The approaches outlined have general applicability to a range of organisms and are discussed in relation to the exploitation of multi-purpose tree species of the tropics. PMID:1385362

Chalmers, K J; Waugh, R; Sprent, J I; Simons, A J; Powell, W

1992-11-01

398

Development of Microsatellite Markers in the Branched Broomrape Phelipanche ramosa L. (Pomel) and Evidence for Host-Associated Genetic Divergence  

PubMed Central

Phelipanche ramosa is a parasitic plant that infects numerous crops worldwide. In Western Europe it recently expanded to a new host crop, oilseed rape, in which it can cause severe yield losses. We developed 13 microsatellite markers for P. ramosa using next-generation 454 sequencing data. The polymorphism at each locus was assessed in a sample of 96 individuals collected in France within 6 fields cultivated with tobacco, hemp or oilseed rape. Two loci were monomorphic. At the other 11 loci, the number of alleles and the expected heterozygosity ranged from 3 to 6 and from 0.31 to 0.60, respectively. Genetic diversity within each cultivated field was very low. The host crop from which individuals were collected was the key factor structuring genetic variation. Individuals collected on oilseed rape were strongly differentiated from individuals collected on hemp or tobacco, which suggests that P. ramosa infecting oilseed rape forms a genetically diverged race. The microsatellites we developed will be useful for population genetics studies and for elucidating host-associated genetic divergence in P. ramosa. PMID:24419096

Le Corre, Valérie; Reibel, Carole; Gibot-Leclerc, Stéphanie

2014-01-01

399

Genetic and physical mapping of sex-linked AFLP markers in Nile tilapia (Oreochromis niloticus).  

PubMed

Identification of the sex-determining genes of the Nile tilapia (Oreochromis niloticus) has important implications for commercial aquaculture. We previously identified an XX/XY sex-determining locus in this species within a 10-cM interval between markers GM201 and UNH995 on linkage group one (LG1). In order to refine this region, we developed new AFLP markers using bulked segregant analysis of the mapping families. We identified three AFLP markers that showed a sex-specific pattern of segregation. All three mapped near, but just outside, the previously identified sex-determining region on LG1. Hybridization of BAC clones containing these markers to chromosome spreads confirmed that the XX/XY sex-determining locus is on one of the small chromosomes in O. niloticus. PMID:20953654

Lee, Bo-Young; Coutanceau, Jean-Pierre; Ozouf-Costaz, Catherine; D'Cotta, Helena; Baroiller, Jean-Francois; Kocher, Thomas D

2011-06-01

400

Assessment of polymorphic genetic markers for multi-locus typing of Cryptosporidium parvum and Cryptosporidium hominis.  

PubMed

The use of high resolution molecular tools to study Cryptosporidium parvum and Cryptosporidium hominis intra-species variation is becoming common practice, but there is currently no consensus in the methods used. The most commonly applied tool is partial gp60 gene sequence analysis. However, multi-locus schemes are acknowledged to improve resolution over analysis of a single locus, which neglects potential re-assortment of genes during the sexual phase of the Cryptosporidium life-cycle. Multi-locus markers have been investigated in isolates from a variety of sampling frames, in varying combinations and using different assays and methods of analysis. To identify the most informative markers as candidates for the development of a standardised multi-locus fragment size-based typing (MLFT) scheme to integrate with epidemiological analyses, we examined the published literature. A total of 31 MLFT studies were found, employing 55 markers of which 45 were applied to both C. parvum and C. hominis. Of the studies, 11 had sufficient raw data, from three or more markers, and a sampling frame containing at least 50 samples, for meaningful in-depth analysis using assessment criteria based on the sampling frame, study size, number of markers investigated in each study, marker characteristics (>2 nucleotide repeats) and the combinations of markers generating all possible multi-locus genotypes. Markers investigated differed between C. hominis and C. parvum. When each scheme was analysed for the fewest markers required to identify 95% of all MLFTs, some redundancy was identified in all schemes; an average redundancy of 40% for C. hominis and 27% for C. parvum. Ranking markers, based on the most productive combinations, identified two different sets of potentially most informative candidate markers, one for each species. These will be subjected to technical evaluation including typability (percentage of samples generating a complete multi-locus type) and discriminatory power by direct fragment size analysis and analysed for correlation with epidemiological data in suitable sampling frames. The establishment of a group of users and agreed subtyping scheme for improved epidemiological and public health investigations of C. parvum and C. hominis will facilitate further developments and consideration of technological advances in a harmonised manner. PMID:22781277

Robinson, Guy; Chalmers, Rachel M

2012-10-01

401

Genetic markers reveal a gradient of hybridization between cape hakes (Merluccius capensis and Merluccius paradoxus) in their sympatric geographic distribution  

NASA Astrophysics Data System (ADS)

The cape hakes Merluccius capensis and Merluccius paradoxus are important fishing resources for African countries such as Namibia and South Africa. In this study we have genetically analyzed adult samples from the overlapping distribution of these species. Eight microsatellite loci, the nuclear 5S rDNA locus and the Cytochrome Oxidase subunit I (COI) gene were employed as molecular markers. A North-South gradient of interspecific hybridization was found, with discordant mitochondrial and nuclear genotypes at the northernmost edge of M. paradoxus distribution. These results suggest intense introgression in North Benguela off the Namibian coast. Independent hake stock assessment is recommended in this region for sustainable management of this valuable resource.

Miralles, Laura; Machado-Schiaffino, Gonzalo; Garcia-Vazquez, Eva

2014-02-01

402

[Genetic markers of individual susceptibility and oxidative stress in subjects exposed to low dose of benzene. Preliminary data].  

PubMed

In the present study we used AOPPs and AGE as early markers of oxidative stress in refinery oil workers. In addition we evaluated whether a genetically determined reduction in the ability to detoxify electrophilic compounds, such as that expected among individuals with glutathione S-transferase (GST) null genotypes might influence the levels of AOPPs thus increasing toxicity. The study was performed on 25 oil refinery workers and in 18 age-matched control subjects. We found a statistically significant increase of AOPPs in exposed workers with respect to controls while AGE levels were not different. Finally serum level of AOPPs and AGE were not correlated with the different GTS genotypes. PMID:23393795

Spatari, G; Abbate, C; Giorgianni, C; Carrieri, M; Sapienza, D; Saitta, S; Barbaro, M

2011-01-01

403

Population genetic structure of island and mainland populations of the quokka, Setonix brachyurus (Macropodidae): a comparison of AFLP and microsatellite markers  

Microsoft Academic Search

Translocation and reintroduction are important tools for the conservation or recovery of species threatened with extinction\\u000a in the wild. However, an understanding of the potential genetic consequences of mixing populations requires an understanding\\u000a of the genetic variation within, and similarities among, donor and recipient populations. Genetic diversity was measured using\\u000a two independent marker systems (microsatellites and AFLPs) for one island

Erika A. Alacs; Peter B. S. Spencer; Paul J. de Tores; Siegfried L. Krauss

2011-01-01

404

The loss of genetic diversity during captive breeding of the endangered sculpin, Trachidermus fasciatus , based on ISSR markers: implications for its conservation  

Microsoft Academic Search

Inter-simple sequence repeat (ISSR) markers were used to determine the genetic variation and genetic differentiation of cultured\\u000a and wild populations of Trachidermus fasciatus, an endangered catadromous fish species in China. Six selected primers were used to amplify DNA samples from 85 individuals,\\u000a and 353 loci were detected. Relatively low genetic diversity was detected in the cultured population (the percentage of

Xiaoxiao Bi; Qiaoli Yang; Tianxiang Gao; Chuangju Li

2011-01-01

405

Genetic diversity and relationships in cultivars of Lolium multiflorum Lam. using sequence-related amplified polymorphism markers.  

PubMed

Sequence-related amplified polymorphism (SRAP) markers were used to analyze and estimate the genetic variability, level of diversity, and relationships among 20 cultivars and strains of annual ryegrass (Lolium multiflorum Lam.). Eighteen SRAP primer combinations generated 334 amplification bands, of which 298 were polymorphic. The polymorphism information content ranged from 0.4715 (me10 + em1) to 0.5000 (me5 + em7), with an average of 0.4921. The genetic similarity coefficient ranged from 0.4304 to 0.8529, and coefficients between 0.65 and 0.90 accounted for 90.00%. The cluster analysis separated the accessions into five groups partly according to their germplasm resource origins. PMID:25501225

Huang, L K; Jiang, X Y; Huang, Q T; Xiao, Y F; Chen, Z H; Zhang, X Q; Miao, J M; Yan, H D

2014-01-01

406

Characterization of the genetic diversity and population structure for the yellow cattle in Taiwan based on microsatellite markers.  

PubMed

In recent years, the population size of Taiwan yellow cattle has drastically declined, even become endangered. A preservation project, Taiwan Yellow Cattle Genetic Preservation Project (TYCGPP), was carried out at the Livestock Research Institute (LRI) Hengchun branch (1988-present). An analysis of intra- and inter- population variability was performed to be the first step to preserve this precious genetic resource. In this work, a total number of 140 individuals selected from the five Taiwan yellow cattle populations were analyzed using 12 microsatellite markers (loci). These markers determined the level of genetic variation within and among populations as well as the phylogenetic structure. The total number of alleles detected (122, 10.28 per locus) and the expected heterozygosity (0.712) indicated that these five populations had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups was 2 (K = 2). Genetic differentiation among clusters was moderate (F ST = 0.095). The result of AMOVA showed that yellow cattle in Taiwan had maintained a high level of within-population genetic differentiation (91%), the remainder being accounted for by differentiation among subpopulations (4%), and by differentiation among regions (5%). The results of STRUCTURE and principal component analysis (PCA) revealed two divergent clusters. The individual unrooted phylogenetic tree showed that some Kinmen yellow cattle in the Hengchun facility (KMHC individuals) were overlapped with Taiwan yellow cattle (TW) and Taiwan yellow cattle Hengchun (HC) populations. Also, they were overlapped with Kinmen × Taiwan (KT) and Kinmen yellow cattle (KM) populations. It is possible that KMHC kept similar phenotypic characteristics and analogous genotypes between TW and KM. A significant inbreeding coefficient (F IS = 0.185; P < 0.01) was detected, suggesting a medium level of inbreeding for yellow cattle in Taiwan. The hypothesis that yellow cattle in Taiwan were derived from two different clusters was also supported by the phylogenetic tree constructed by the UPGMA, indicating that the yellow cattle in Taiwan and in Kinmen should be treated as two different management units. This result will be applied to maintain a good level of genetic variability and rusticity (stress-resistance) and to avoid further inbreeding for yellow cattle population in Taiwan. PMID:24813218

Tu, Po-An; Lin, Der-Yuh; Li, Guang-Fu; Huang, Jan-Chi; Wang, De-Chi; Wang, Pei-Hwa

2014-01-01

407

Development of new genomic microsatellite markers from robusta coffee (Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies  

PubMed Central

Background Species-specific microsatellite markers are desirable for genetic studies and to harness the potential of MAS-based breeding for genetic improvement. Limited availability of such markers for coffee, one of the most important beverage tree crops, warrants newer efforts to develop additional microsatellite markers that can be effectively deployed in genetic analysis and coffee improvement programs. The pres